- Duplication rate
- Coverage per target w/ w/o duplicates
- Number of novel variants
- AFS
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T1D-RA targeted regulatory sequencing
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:b8c95e1d1caf12d20c692fe3c4877d38bf4c80dd5e1c4fbc667ec961c6afbc9a" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ | |
| { | |
| "cell_type": "heading", | |
| "level": 3, | |
| "metadata": {}, | |
| "source": [ | |
| "What is the allele frequency spectrum for _known_, on-target variants?" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%bash\n", | |
| "\n", | |
| "gemini query \\\n", | |
| " -q \"select aaf from variants where on_target = 1 and in_dbsnp = 1\" \\\n", | |
| " t1d-ra.300samples.vqsr.db \\\n", | |
| "| grep -v None > aaf_known" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 23 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%load_ext rmagic" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "The rmagic extension is already loaded. To reload it, use:\n", | |
| " %reload_ext rmagic\n" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 11 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%R\n", | |
| "\n", | |
| "aaf <- read.table('aaf_known', header=F)\n", | |
| "hist(aaf[,1], breaks=20, main=\"AFS for known, on-target variants\")" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "metadata": {}, | |
| "output_type": "display_data", | |
| "png": 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BDx06NK7LkCZMmCBTpkyJ5BH9ZMuWLdKxY8foWTxHAAEEEEAgMIFQ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\ngg==\n" | |
| } | |
| ], | |
| "prompt_number": 24 | |
| }, | |
| { | |
| "cell_type": "heading", | |
| "level": 3, | |
| "metadata": {}, | |
| "source": [ | |
| "What is the allele frequency spectrum for _novel_, on-target variants?" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%bash\n", | |
| "\n", | |
| "gemini query \\\n", | |
| " -q \"select aaf from variants where on_target = 1 and in_dbsnp = 0\" \\\n", | |
| " t1d-ra.300samples.vqsr.db \\\n", | |
| "| grep -v None > aaf_novel" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 25 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%R\n", | |
| "\n", | |
| "aaf <- read.table('aaf_novel', header=F)\n", | |
| "hist(aaf[,1], breaks=20, main=\"AFS for known, on-target variants\")" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "metadata": {}, | |
| "output_type": "display_data", | |
| "png": 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BOAB0skQAAQQQQIAAzDGAAAIIIIBAAAIE4ADQyRIBBBBAAAECMMcAAggggAAC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\n" | |
| } | |
| ], | |
| "prompt_number": 26 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| } | |
| ], | |
| "metadata": {} | |
| } | |
| ] | |
| } |
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| # /Users/arq5x/Documents/Projects/QuinlanLab/Collaboration/T1D-RA-H3K4me3-Seq/vcf/72-samples | |
| python comparison-to-immunochip.py t1d-ra.72samples.vqsr.db > t1d-ra.exp.ontarget.hg19.bed | |
| cut -f 1-3 t1d-ra.exp.ontarget.hg19.bed | awk 'NR>1' > t1d-ra.exp.ontarget.hg19.bed3 | |
| liftOver t1d-ra.exp.ontarget.hg19.bed3 hg19ToHg18.over.chain.gz t1d-ra.exp.ontarget.hg18.bed3 unmapped | |
| (cat t1d-ra.exp.ontarget.hg18.bed3 | awk '{print $0"\tmapped"}'; awk '{if (NF==4) {print $0"\tunmapped"}}' unmapped) | sort -k4,4n > lifted.bed | |
| paste t1d-ra.exp.ontarget.hg19.bed3 lifted.bed > full | |
| paste t1d-ra.exp.ontarget.hg19.bed full > t1d-ra.exp.ontarget.hg19.and.hg18.bed |
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| args <- commandArgs(TRUE) | |
| # Get a list of the bedtools output files you'd like to read in | |
| print(files <- list.files(pattern="cov.genomewide.txt$")) | |
| # Create lists to hold coverage and cumulative coverage for each alignment, | |
| # and read the data into these lists. | |
| cov <- list() | |
| cov_cumul <- list() | |
| for (i in 1:length(files)) { | |
| cov[[i]] <- read.table(files[i]) | |
| cov_cumul[[i]] <- 1-cumsum(cov[[i]][,5]) | |
| } | |
| #cov = read.table(file); | |
| #library(RColorBrewer) | |
| cols <- rainbow(length(cov)) | |
| print(labs <- gsub("\\.cov\\.genomewide\\.txt", "", files, perl=TRUE), sep="") | |
| # Create a cumulative distribution from the "raw" hist (truncate at depth >=1000) | |
| #cov_cumul = 1 - cumsum(cov[,5]); | |
| # Create plot area, but do not plot anything. Add gridlines and axis labels. | |
| plot(cov[[1]][2:401, 2], cov_cumul[[1]][1:400], type='n', xlab="Depth", ylab="Fraction of capture target bases with depth", ylim=c(0,1.0), main="Target Region Coverage") | |
| abline(v = 20, col = "gray60") | |
| abline(v = 50, col = "gray60") | |
| abline(v = 80, col = "gray60") | |
| abline(v = 100, col = "gray60") | |
| abline(h = 0.50, col = "gray60") | |
| abline(h = 0.90, col = "gray60") | |
| axis(1, at=c(20,50,80), labels=c(20,50,80)) | |
| axis(2, at=c(0.90), labels=c(0.90)) | |
| axis(2, at=c(0.50), labels=c(0.50)) | |
| # Actually plot the data for each of the alignments (stored in the lists). | |
| for (i in 1:length(cov)) points(cov[[i]][2:401, 2], cov_cumul[[i]][1:400], type='l', lwd=3, col=cols[i]) | |
| # Add a legend using the nice sample labeles rather than the full filenames. | |
| legend("topright", legend=labs, col=cols, lty=1, lwd=4) | |
| # Create a plot of the CDF | |
| #plot(cov[2:401,2], cov_cumul[1:400], col='darkgreen', type='l', lwd=2, | |
| # xlab="Depth", ylab="Fraction of genome >= depth", ylim=c(0,1.0), | |
| # main=file | |
| #) | |
| #abline(v = 20, col = "gray60") | |
| #abline(v = 50, col = "gray60") | |
| #abline(v = 80, col = "gray60") | |
| #abline(v = 100, col = "gray60") | |
| #abline(h = 0.90, col = "gray60") | |
| #axis(1, at=c(20,50,80), labels=c(20,50,80)) | |
| #axis(2, at=c(0.90), labels=c(0.90)) | |
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| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| for sample in `echo $SAMPLES`; | |
| do | |
| cd $T1DHOME | |
| grep all coverage/$sample.cov.txt > coverage/$sample.cov.genomewide.txt | |
| done | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/coverage | |
| cd $T1DHOME | |
| for rundir in `ls -d *run* | grep -v pdf`; | |
| do | |
| cd $rundir | |
| Rscript ../plotter.multi.R $rundir | |
| mv Rplots.pdf ../$rundir.coverage.cdf.pdf | |
| cd .. | |
| done | |
| gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=allruns.coverage.pdf *.coverage.cdf.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=t1d-run1.pdf coverage/t1d-run1/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=t1d-run1-v3.pdf coverage/t1d-run1-v3/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=t1d-run2a.pdf coverage/t1d-run2a/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=t1d-run4a.pdf coverage/t1d-run4a/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run2.pdf ra-run2/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run3.pdf ra-run3/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run4.pdf ra-run4/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run5.pdf ra-run5/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run6.pdf ra-run6/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run7.pdf ra-run7/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run8.pdf ra-run8/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run9.pdf ra-run9/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run10.pdf ra-run10/*.pdf | |
| #gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=ra-run11.pdf ra-run11/*.pdf |
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| export SAMPLES="t1d-run2a-redo/40322601 \ | |
| t1d-run2a-redo/40322602 \ | |
| t1d-run2a-redo/40322604 \ | |
| t1d-run2a-redo/40473801 \ | |
| t1d-run2a-redo/40473802 \ | |
| t1d-run2a-redo/40473803 \ | |
| t1d-run2a-redo/41789801 \ | |
| t1d-run2a-redo/41789802 \ | |
| t1d-run2a-redo/41789803 \ | |
| t1d-run2a-redo/42390801 \ | |
| t1d-run2a-redo/42390802 \ | |
| t1d-run2a-redo/42390803 \ | |
| t1d-run2a-redo/43131301 \ | |
| t1d-run2a-redo/43131302 \ | |
| t1d-run2a-redo/43131303 \ | |
| t1d-run2a-redo/43821501 \ | |
| t1d-run2a-redo/43821502 \ | |
| t1d-run2a-redo/43821503 \ | |
| t1d-run2a-redo/48657901 \ | |
| t1d-run2a-redo/48657902 \ | |
| t1d-run2a-redo/48657903 \ | |
| t1d-run2a-redo/48917101 \ | |
| t1d-run2a-redo/48917102 \ | |
| t1d-run2a-redo/48917104 \ | |
| t1d-run5b-redo/40612301 \ | |
| t1d-run5b-redo/40612302 \ | |
| t1d-run5b-redo/40612303 \ | |
| t1d-run5b-redo/40705901 \ | |
| t1d-run5b-redo/40705902 \ | |
| t1d-run5b-redo/40705904 \ | |
| t1d-run5b-redo/40761201 \ | |
| t1d-run5b-redo/40761202 \ | |
| t1d-run5b-redo/40761203 \ | |
| t1d-run5b-redo/40969901 \ | |
| t1d-run5b-redo/40969902 \ | |
| t1d-run5b-redo/40969904 \ | |
| t1d-run5b-redo/43131601 \ | |
| t1d-run5b-redo/43131602 \ | |
| t1d-run5b-redo/43131604 \ | |
| t1d-run5b-redo/45637601 \ | |
| t1d-run5b-redo/45637602 \ | |
| t1d-run5b-redo/45637604 \ | |
| t1d-run5b-redo/48796901 \ | |
| t1d-run5b-redo/48796902 \ | |
| t1d-run5b-redo/48796903 \ | |
| t1d-run5b-redo/49798101 \ | |
| t1d-run5b-redo/49798102 \ | |
| t1d-run5b-redo/49798103" | |
| export SAMPLES2=" | |
| ra-run10/217 \ | |
| ra-run10/218 \ | |
| ra-run10/219 \ | |
| ra-run10/220 \ | |
| ra-run10/221 \ | |
| ra-run10/222 \ | |
| ra-run10/223 \ | |
| ra-run10/224 \ | |
| ra-run10/225 \ | |
| ra-run10/226 \ | |
| ra-run10/227 \ | |
| ra-run10/228 \ | |
| ra-run10/229 \ | |
| ra-run10/230 \ | |
| ra-run10/231 \ | |
| ra-run10/232 \ | |
| ra-run10/233 \ | |
| ra-run10/234 \ | |
| ra-run10/235 \ | |
| ra-run10/236 \ | |
| ra-run10/237 \ | |
| ra-run10/238 \ | |
| ra-run10/239 \ | |
| ra-run10/240 \ | |
| ra-run1/1 \ | |
| ra-run1/10 \ | |
| ra-run1/11 \ | |
| ra-run1/12 \ | |
| ra-run11/241 \ | |
| ra-run11/242 \ | |
| ra-run11/243 \ | |
| ra-run11/244 \ | |
| ra-run11/245 \ | |
| ra-run11/246 \ | |
| ra-run11/247 \ | |
| ra-run11/248 \ | |
| ra-run11/249 \ | |
| ra-run11/250 \ | |
| ra-run11/251 \ | |
| ra-run11/252 \ | |
| ra-run11/253 \ | |
| ra-run11/254 \ | |
| ra-run11/255 \ | |
| ra-run11/256 \ | |
| ra-run11/257 \ | |
| ra-run11/258 \ | |
| ra-run11/259 \ | |
| ra-run11/260 \ | |
| ra-run11/261 \ | |
| ra-run11/262 \ | |
| ra-run11/263 \ | |
| ra-run11/264 \ | |
| ra-run1/13 \ | |
| ra-run1/14 \ | |
| ra-run1/15 \ | |
| ra-run1/16 \ | |
| ra-run1/17 \ | |
| ra-run1/18 \ | |
| ra-run1/19 \ | |
| ra-run1/2 \ | |
| ra-run1/20 \ | |
| ra-run1/21 \ | |
| ra-run1/22 \ | |
| ra-run12/265 \ | |
| ra-run12/266 \ | |
| ra-run12/267 \ | |
| ra-run12/268 \ | |
| ra-run12/269 \ | |
| ra-run12/270 \ | |
| ra-run12/271 \ | |
| ra-run12/272 \ | |
| ra-run12/273 \ | |
| ra-run12/274 \ | |
| ra-run12/275 \ | |
| ra-run12/276 \ | |
| ra-run12/277 \ | |
| ra-run12/278 \ | |
| ra-run12/279 \ | |
| ra-run12/280 \ | |
| ra-run12/281 \ | |
| ra-run12/282 \ | |
| ra-run12/283 \ | |
| ra-run12/284 \ | |
| ra-run12/285 \ | |
| ra-run12/286 \ | |
| ra-run12/287 \ | |
| ra-run12/288 \ | |
| ra-run1/23 \ | |
| ra-run1/24 \ | |
| ra-run1/3 \ | |
| ra-run13/289 \ | |
| ra-run13/290 \ | |
| ra-run13/291 \ | |
| ra-run13/292 \ | |
| ra-run13/293 \ | |
| ra-run13/294 \ | |
| ra-run13/295 \ | |
| ra-run13/296 \ | |
| ra-run13/297 \ | |
| ra-run13/298 \ | |
| ra-run13/299 \ | |
| ra-run13/300 \ | |
| ra-run13/301 \ | |
| ra-run13/302 \ | |
| ra-run13/303 \ | |
| ra-run13/304 \ | |
| ra-run13/305 \ | |
| ra-run13/306 \ | |
| ra-run13/307 \ | |
| ra-run13/308 \ | |
| ra-run13/309 \ | |
| ra-run13/310 \ | |
| ra-run13/311 \ | |
| ra-run13/312 \ | |
| ra-run1/4 \ | |
| ra-run14/313 \ | |
| ra-run14/314 \ | |
| ra-run14/315 \ | |
| ra-run14/316 \ | |
| ra-run14/317 \ | |
| ra-run14/318 \ | |
| ra-run14/319 \ | |
| ra-run14/320 \ | |
| ra-run14/321 \ | |
| ra-run14/322 \ | |
| ra-run14/323 \ | |
| ra-run14/324 \ | |
| ra-run14/325 \ | |
| ra-run14/326 \ | |
| ra-run14/327 \ | |
| ra-run14/328 \ | |
| ra-run14/329 \ | |
| ra-run14/330 \ | |
| ra-run14/331 \ | |
| ra-run14/332 \ | |
| ra-run14/333 \ | |
| ra-run14/334 \ | |
| ra-run14/335 \ | |
| ra-run14/336 \ | |
| ra-run1/5 \ | |
| ra-run15/337 \ | |
| ra-run15/338 \ | |
| ra-run15/339 \ | |
| ra-run15/340 \ | |
| ra-run15/341 \ | |
| ra-run15/342 \ | |
| ra-run15/343 \ | |
| ra-run15/344 \ | |
| ra-run15/345 \ | |
| ra-run15/346 \ | |
| ra-run15/347 \ | |
| ra-run15/348 \ | |
| ra-run15/349 \ | |
| ra-run15/350 \ | |
| ra-run15/351 \ | |
| ra-run15/352 \ | |
| ra-run15/353 \ | |
| ra-run15/354 \ | |
| ra-run15/355 \ | |
| ra-run15/356 \ | |
| ra-run15/357 \ | |
| ra-run15/358 \ | |
| ra-run15/359 \ | |
| ra-run15/360 \ | |
| ra-run1/6 \ | |
| ra-run16/361 \ | |
| ra-run16/362 \ | |
| ra-run16/363 \ | |
| ra-run16/364 \ | |
| ra-run16/365 \ | |
| ra-run16/366 \ | |
| ra-run16/367 \ | |
| ra-run16/368 \ | |
| ra-run16/369 \ | |
| ra-run16/370 \ | |
| ra-run16/371 \ | |
| ra-run16/372 \ | |
| ra-run16/373 \ | |
| ra-run16/374 \ | |
| ra-run16/375 \ | |
| ra-run16/376 \ | |
| ra-run16/377 \ | |
| ra-run16/378 \ | |
| ra-run16/379 \ | |
| ra-run16/380 \ | |
| ra-run16/381 \ | |
| ra-run16/382 \ | |
| ra-run16/383 \ | |
| ra-run16/384 \ | |
| ra-run1/7 \ | |
| ra-run1/8 \ | |
| ra-run1/9 \ | |
| ra-run2/25 \ | |
| ra-run2/26 \ | |
| ra-run2/27 \ | |
| ra-run2/28 \ | |
| ra-run2/29 \ | |
| ra-run2/30 \ | |
| ra-run2/31 \ | |
| ra-run2/32 \ | |
| ra-run2/33 \ | |
| ra-run2/34 \ | |
| ra-run2/35 \ | |
| ra-run2/36 \ | |
| ra-run2/37 \ | |
| ra-run2/38 \ | |
| ra-run2/39 \ | |
| ra-run2/40 \ | |
| ra-run2/41 \ | |
| ra-run2/42 \ | |
| ra-run2/43 \ | |
| ra-run2/44 \ | |
| ra-run2/45 \ | |
| ra-run2/46 \ | |
| ra-run2/47 \ | |
| ra-run2/48 \ | |
| ra-run3/49 \ | |
| ra-run3/50 \ | |
| ra-run3/51 \ | |
| ra-run3/52 \ | |
| ra-run3/53 \ | |
| ra-run3/54 \ | |
| ra-run3/55 \ | |
| ra-run3/56 \ | |
| ra-run3/57 \ | |
| ra-run3/58 \ | |
| ra-run3/59 \ | |
| ra-run3/60 \ | |
| ra-run3/61 \ | |
| ra-run3/62 \ | |
| ra-run3/63 \ | |
| ra-run3/64 \ | |
| ra-run3/65 \ | |
| ra-run3/66 \ | |
| ra-run3/67 \ | |
| ra-run3/68 \ | |
| ra-run3/69 \ | |
| ra-run3/70 \ | |
| ra-run3/71 \ | |
| ra-run3/72 \ | |
| ra-run4/73 \ | |
| ra-run4/74 \ | |
| ra-run4/75 \ | |
| ra-run4/76 \ | |
| ra-run4/77 \ | |
| ra-run4/78 \ | |
| ra-run4/79 \ | |
| ra-run4/80 \ | |
| ra-run4/81 \ | |
| ra-run4/82 \ | |
| ra-run4/83 \ | |
| ra-run4/84 \ | |
| ra-run4/85 \ | |
| ra-run4/86 \ | |
| ra-run4/87 \ | |
| ra-run4/88 \ | |
| ra-run4/89 \ | |
| ra-run4/90 \ | |
| ra-run4/91 \ | |
| ra-run4/92 \ | |
| ra-run4/93 \ | |
| ra-run4/94 \ | |
| ra-run4/95 \ | |
| ra-run4/96 \ | |
| ra-run5/100 \ | |
| ra-run5/101 \ | |
| ra-run5/102 \ | |
| ra-run5/103 \ | |
| ra-run5/104 \ | |
| ra-run5/105 \ | |
| ra-run5/106 \ | |
| ra-run5/107 \ | |
| ra-run5/108 \ | |
| ra-run5/145 \ | |
| ra-run5/146 \ | |
| ra-run5/147 \ | |
| ra-run5/148 \ | |
| ra-run5/149 \ | |
| ra-run5/150 \ | |
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| ra-run5/155 \ | |
| ra-run5/156 \ | |
| ra-run5/97 \ | |
| ra-run5/98 \ | |
| ra-run5/99 \ | |
| ra-run6/109 \ | |
| ra-run6/110 \ | |
| ra-run6/111 \ | |
| ra-run6/112 \ | |
| ra-run6/113 \ | |
| ra-run6/114 \ | |
| ra-run6/115 \ | |
| ra-run6/116 \ | |
| ra-run6/117 \ | |
| ra-run6/118 \ | |
| ra-run6/119 \ | |
| ra-run6/120 \ | |
| ra-run6/121 \ | |
| ra-run6/122 \ | |
| ra-run6/123 \ | |
| ra-run6/124 \ | |
| ra-run6/125 \ | |
| ra-run6/126 \ | |
| ra-run6/127 \ | |
| ra-run6/128 \ | |
| ra-run6/129 \ | |
| ra-run6/130 \ | |
| ra-run6/131 \ | |
| ra-run6/132 \ | |
| ra-run7/133 \ | |
| ra-run7/134 \ | |
| ra-run7/135 \ | |
| ra-run7/136 \ | |
| ra-run7/137 \ | |
| ra-run7/138 \ | |
| ra-run7/139 \ | |
| ra-run7/140 \ | |
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| ra-run7/142 \ | |
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| ra-run7/157 \ | |
| ra-run7/158 \ | |
| ra-run7/159 \ | |
| ra-run7/160 \ | |
| ra-run7/161 \ | |
| ra-run7/162 \ | |
| ra-run7/163 \ | |
| ra-run7/164 \ | |
| ra-run7/165 \ | |
| ra-run7/166 \ | |
| ra-run7/167 \ | |
| ra-run7/168 \ | |
| ra-run8/169 \ | |
| ra-run8/170 \ | |
| ra-run8/171 \ | |
| ra-run8/172 \ | |
| ra-run8/173 \ | |
| ra-run8/174 \ | |
| ra-run8/175 \ | |
| ra-run8/176 \ | |
| ra-run8/177 \ | |
| ra-run8/178 \ | |
| ra-run8/179 \ | |
| ra-run8/180 \ | |
| ra-run8/181 \ | |
| ra-run8/182 \ | |
| ra-run8/183 \ | |
| ra-run8/184 \ | |
| ra-run8/185 \ | |
| ra-run8/186 \ | |
| ra-run8/187 \ | |
| ra-run8/188 \ | |
| ra-run8/189 \ | |
| ra-run8/190 \ | |
| ra-run8/191 \ | |
| ra-run8/192 \ | |
| ra-run9/193 \ | |
| ra-run9/194 \ | |
| ra-run9/195 \ | |
| ra-run9/196 \ | |
| ra-run9/197 \ | |
| ra-run9/198 \ | |
| ra-run9/199 \ | |
| ra-run9/200 \ | |
| ra-run9/201 \ | |
| ra-run9/202 \ | |
| ra-run9/203 \ | |
| ra-run9/204 \ | |
| ra-run9/205 \ | |
| ra-run9/206 \ | |
| ra-run9/207 \ | |
| ra-run9/208 \ | |
| ra-run9/209 \ | |
| ra-run9/210 \ | |
| ra-run9/211 \ | |
| ra-run9/212 \ | |
| ra-run9/213 \ | |
| ra-run9/214 \ | |
| ra-run9/215 \ | |
| ra-run9/216 \ | |
| t1d-run10a/42192101 \ | |
| t1d-run10a/42192102 \ | |
| t1d-run10a/42192104 \ | |
| t1d-run10a/42552101 \ | |
| t1d-run10a/42552102 \ | |
| t1d-run10a/42552104 \ | |
| t1d-run10a/42933801 \ | |
| t1d-run10a/42933802 \ | |
| t1d-run10a/42933804 \ | |
| t1d-run10a/45994201 \ | |
| t1d-run10a/45994202 \ | |
| t1d-run10a/45994203 \ | |
| t1d-run10a/46197301 \ | |
| t1d-run10a/46197302 \ | |
| t1d-run10a/46197304 \ | |
| t1d-run10a/47956601 \ | |
| t1d-run10a/47956602 \ | |
| t1d-run10a/47956603 \ | |
| t1d-run10a/48219501 \ | |
| t1d-run10a/48219502 \ | |
| t1d-run10a/48219503 \ | |
| t1d-run10a/48515001 \ | |
| t1d-run10a/48515002 \ | |
| t1d-run10a/48515003 \ | |
| t1d-run10b/40010401 \ | |
| t1d-run10b/40010402 \ | |
| t1d-run10b/40010404 \ | |
| t1d-run10b/41245501 \ | |
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| t1d-run10b/41245504 \ | |
| t1d-run10b/43266601 \ | |
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| t1d-run10b/43266604 \ | |
| t1d-run10b/44181401 \ | |
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| t1d-run10b/44181403 \ | |
| t1d-run10b/45158201 \ | |
| t1d-run10b/45158202 \ | |
| t1d-run10b/45158203 \ | |
| t1d-run10b/45320801 \ | |
| t1d-run10b/45320802 \ | |
| t1d-run10b/45320804 \ | |
| t1d-run10b/45541601 \ | |
| t1d-run10b/45541602 \ | |
| t1d-run10b/45541604 \ | |
| t1d-run10b/45925501 \ | |
| t1d-run10b/45925502 \ | |
| t1d-run10b/45925503 \ | |
| t1d-run11/40983201 \ | |
| t1d-run11/40983202 \ | |
| t1d-run11/40983204 \ | |
| t1d-run11/44005001 \ | |
| t1d-run11/44005002 \ | |
| t1d-run11/44005003 \ | |
| t1d-run11/44495201 \ | |
| t1d-run11/44495202 \ | |
| t1d-run11/44495203 \ | |
| t1d-run11/44997901 \ | |
| t1d-run11/44997902 \ | |
| t1d-run11/44997904 \ | |
| t1d-run11/45383001 \ | |
| t1d-run11/45383002 \ | |
| t1d-run11/45383004 \ | |
| t1d-run11/46966301 \ | |
| t1d-run11/46966302 \ | |
| t1d-run11/46966303 \ | |
| t1d-run11/47585201 \ | |
| t1d-run11/47585202 \ | |
| t1d-run11/47585203 \ | |
| t1d-run11/47789101 \ | |
| t1d-run11/47789102 \ | |
| t1d-run11/47789103 \ | |
| t1d-run1/41032601 \ | |
| t1d-run1/41032602 \ | |
| t1d-run1/41032603 \ | |
| t1d-run1/42044401 \ | |
| t1d-run1/42044402 \ | |
| t1d-run1/42044403 \ | |
| t1d-run1/44003301 \ | |
| t1d-run1/44003302 \ | |
| t1d-run1/44003304 \ | |
| t1d-run1/44123901 \ | |
| t1d-run1/44123902 \ | |
| t1d-run1/44123903 \ | |
| t1d-run1/44143001 \ | |
| t1d-run1/44143002 \ | |
| t1d-run1/44143004 \ | |
| t1d-run1/46628201 \ | |
| t1d-run1/46628202 \ | |
| t1d-run1/46628204 \ | |
| t1d-run1/47960801 \ | |
| t1d-run1/47960802 \ | |
| t1d-run1/47960803 \ | |
| t1d-run1/48094101 \ | |
| t1d-run1/48094102 \ | |
| t1d-run1/48094104 \ | |
| t1d-run1-v3/41032601 \ | |
| t1d-run1-v3/41032602 \ | |
| t1d-run1-v3/41032603 \ | |
| t1d-run1-v3/42044401 \ | |
| t1d-run1-v3/42044402 \ | |
| t1d-run1-v3/42044403 \ | |
| t1d-run1-v3/44003301 \ | |
| t1d-run1-v3/44003302 \ | |
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| t1d-run1-v3/44123901 \ | |
| t1d-run1-v3/44123902 \ | |
| t1d-run1-v3/44123903 \ | |
| t1d-run1-v3/44143001 \ | |
| t1d-run1-v3/44143002 \ | |
| t1d-run1-v3/44143004 \ | |
| t1d-run1-v3/46628201 \ | |
| t1d-run1-v3/46628202 \ | |
| t1d-run1-v3/46628204 \ | |
| t1d-run1-v3/47960801 \ | |
| t1d-run1-v3/47960802 \ | |
| t1d-run1-v3/47960803 \ | |
| t1d-run1-v3/48094101 \ | |
| t1d-run1-v3/48094102 \ | |
| t1d-run1-v3/48094104 \ | |
| t1d-run2a/40322601 \ | |
| t1d-run2a/40322602 \ | |
| t1d-run2a/40322604 \ | |
| t1d-run2a/40473801 \ | |
| t1d-run2a/40473802 \ | |
| t1d-run2a/40473803 \ | |
| t1d-run2a/41789801 \ | |
| t1d-run2a/41789802 \ | |
| t1d-run2a/41789803 \ | |
| t1d-run2a/42390801 \ | |
| t1d-run2a/42390802 \ | |
| t1d-run2a/42390803 \ | |
| t1d-run2a/43131301 \ | |
| t1d-run2a/43131302 \ | |
| t1d-run2a/43131303 \ | |
| t1d-run2a/43821501 \ | |
| t1d-run2a/43821502 \ | |
| t1d-run2a/43821503 \ | |
| t1d-run2a/48657801 \ | |
| t1d-run2a/48657902 \ | |
| t1d-run2a/48657903 \ | |
| t1d-run2a/48917101 \ | |
| t1d-run2a/48917102 \ | |
| t1d-run2a/48917104 \ | |
| t1d-run2a-redo/40322601 \ | |
| t1d-run2a-redo/40322602 \ | |
| t1d-run2a-redo/40322604 \ | |
| t1d-run2a-redo/40473801 \ | |
| t1d-run2a-redo/40473802 \ | |
| t1d-run2a-redo/40473803 \ | |
| t1d-run2a-redo/41789801 \ | |
| t1d-run2a-redo/41789802 \ | |
| t1d-run2a-redo/41789803 \ | |
| t1d-run2a-redo/42390801 \ | |
| t1d-run2a-redo/42390802 \ | |
| t1d-run2a-redo/42390803 \ | |
| t1d-run2a-redo/43131301 \ | |
| t1d-run2a-redo/43131302 \ | |
| t1d-run2a-redo/43131303 \ | |
| t1d-run2a-redo/43821501 \ | |
| t1d-run2a-redo/43821502 \ | |
| t1d-run2a-redo/43821503 \ | |
| t1d-run2a-redo/48657901 \ | |
| t1d-run2a-redo/48657902 \ | |
| t1d-run2a-redo/48657903 \ | |
| t1d-run2a-redo/48917101 \ | |
| t1d-run2a-redo/48917102 \ | |
| t1d-run2a-redo/48917104 \ | |
| t1d-run2b/41050801 \ | |
| t1d-run2b/41050802 \ | |
| t1d-run2b/41050803 \ | |
| t1d-run2b/43293801 \ | |
| t1d-run2b/43293802 \ | |
| t1d-run2b/43293804 \ | |
| t1d-run2b/44213301 \ | |
| t1d-run2b/44213302 \ | |
| t1d-run2b/44213303 \ | |
| t1d-run2b/44724901 \ | |
| t1d-run2b/44724902 \ | |
| t1d-run2b/44724903 \ | |
| t1d-run2b/45676501 \ | |
| t1d-run2b/45676502 \ | |
| t1d-run2b/45676504 \ | |
| t1d-run2b/45808601 \ | |
| t1d-run2b/45808602 \ | |
| t1d-run2b/45808604 \ | |
| t1d-run2b/46291001 \ | |
| t1d-run2b/46291002 \ | |
| t1d-run2b/46291003 \ | |
| t1d-run2b/47439601 \ | |
| t1d-run2b/47439602 \ | |
| t1d-run2b/47439604 \ | |
| t1d-run3a/40458101 \ | |
| t1d-run3a/40458102 \ | |
| t1d-run3a/40458103 \ | |
| t1d-run3a/41073901 \ | |
| t1d-run3a/41073902 \ | |
| t1d-run3a/41073903 \ | |
| t1d-run3a/41075701 \ | |
| t1d-run3a/41075702 \ | |
| t1d-run3a/41075704 \ | |
| t1d-run3a/42153401 \ | |
| t1d-run3a/42153402 \ | |
| t1d-run3a/42153404 \ | |
| t1d-run3a/43673001 \ | |
| t1d-run3a/43673002 \ | |
| t1d-run3a/43673003 \ | |
| t1d-run3a/44270401 \ | |
| t1d-run3a/44270402 \ | |
| t1d-run3a/44270404 \ | |
| t1d-run3a/44638201 \ | |
| t1d-run3a/44638202 \ | |
| t1d-run3a/44638203 \ | |
| t1d-run3a/45789703 \ | |
| t1d-run3a/46789701 \ | |
| t1d-run3a/46789702 \ | |
| t1d-run3b/40946401 \ | |
| t1d-run3b/40946402 \ | |
| t1d-run3b/40946403 \ | |
| t1d-run3b/42448401 \ | |
| t1d-run3b/42448402 \ | |
| t1d-run3b/42448403 \ | |
| t1d-run3b/44609801 \ | |
| t1d-run3b/44609802 \ | |
| t1d-run3b/44609803 \ | |
| t1d-run3b/45432701 \ | |
| t1d-run3b/45432702 \ | |
| t1d-run3b/45432703 \ | |
| t1d-run3b/47076101 \ | |
| t1d-run3b/47076102 \ | |
| t1d-run3b/47076103 \ | |
| t1d-run3b/47203001 \ | |
| t1d-run3b/47203002 \ | |
| t1d-run3b/47203003 \ | |
| t1d-run3b/47384401 \ | |
| t1d-run3b/47384402 \ | |
| t1d-run3b/47384404 \ | |
| t1d-run3b/49699501 \ | |
| t1d-run3b/49699502 \ | |
| t1d-run3b/49699503 \ | |
| t1d-run4a/40117101 \ | |
| t1d-run4a/40117102 \ | |
| t1d-run4a/40117104 \ | |
| t1d-run4a/42407801 \ | |
| t1d-run4a/42407802 \ | |
| t1d-run4a/42407804 \ | |
| t1d-run4a/45229501 \ | |
| t1d-run4a/45229502 \ | |
| t1d-run4a/45229504 \ | |
| t1d-run4a/45688801 \ | |
| t1d-run4a/45688802 \ | |
| t1d-run4a/45688804 \ | |
| t1d-run4a/46399401 \ | |
| t1d-run4a/46399402 \ | |
| t1d-run4a/46399404 \ | |
| t1d-run4a/47786201 \ | |
| t1d-run4a/47786202 \ | |
| t1d-run4a/47786203 \ | |
| t1d-run4a/49436401 \ | |
| t1d-run4a/49436402 \ | |
| t1d-run4a/49436403 \ | |
| t1d-run4a/49737801 \ | |
| t1d-run4a/49737802 \ | |
| t1d-run4a/49737804 \ | |
| t1d-run4b/41209801 \ | |
| t1d-run4b/41209802 \ | |
| t1d-run4b/41209804 \ | |
| t1d-run4b/42239101 \ | |
| t1d-run4b/42239102 \ | |
| t1d-run4b/42239104 \ | |
| t1d-run4b/47791201 \ | |
| t1d-run4b/47791202 \ | |
| t1d-run4b/47791203 \ | |
| t1d-run4b/48842701 \ | |
| t1d-run4b/48842702 \ | |
| t1d-run4b/48842704 \ | |
| t1d-run4b/49423501 \ | |
| t1d-run4b/49423502 \ | |
| t1d-run4b/49423503 \ | |
| t1d-run4b/49484401 \ | |
| t1d-run4b/49484402 \ | |
| t1d-run4b/49484404 \ | |
| t1d-run4b/49530101 \ | |
| t1d-run4b/49530102 \ | |
| t1d-run4b/49530104 \ | |
| t1d-run4b/49713901 \ | |
| t1d-run4b/49713902 \ | |
| t1d-run4b/49713904 \ | |
| t1d-run5a/40203301 \ | |
| t1d-run5a/40203302 \ | |
| t1d-run5a/40203307 \ | |
| t1d-run5a/40712001 \ | |
| t1d-run5a/40712002 \ | |
| t1d-run5a/40712003 \ | |
| t1d-run5a/42545801 \ | |
| t1d-run5a/42545802 \ | |
| t1d-run5a/42545803 \ | |
| t1d-run5a/43199001 \ | |
| t1d-run5a/43199002 \ | |
| t1d-run5a/43199003 \ | |
| t1d-run5a/44194701 \ | |
| t1d-run5a/44194702 \ | |
| t1d-run5a/44194703 \ | |
| t1d-run5a/44673501 \ | |
| t1d-run5a/44673502 \ | |
| t1d-run5a/44673507 \ | |
| t1d-run5a/47948201 \ | |
| t1d-run5a/47948202 \ | |
| t1d-run5a/47948203 \ | |
| t1d-run5a/49055901 \ | |
| t1d-run5a/49055902 \ | |
| t1d-run5a/49055903 \ | |
| t1d-run5b/40612302 \ | |
| t1d-run5b/40612301 \ | |
| t1d-run5b/40612303 \ | |
| t1d-run5b/40705901 \ | |
| t1d-run5b/40705902 \ | |
| t1d-run5b/40705904 \ | |
| t1d-run5b/40761201 \ | |
| t1d-run5b/40761202 \ | |
| t1d-run5b/40761203 \ | |
| t1d-run5b/40969901 \ | |
| t1d-run5b/40969902 \ | |
| t1d-run5b/40969904 \ | |
| t1d-run5b/43131601 \ | |
| t1d-run5b/43131602 \ | |
| t1d-run5b/43131604 \ | |
| t1d-run5b/45637601 \ | |
| t1d-run5b/45637602 \ | |
| t1d-run5b/45637604 \ | |
| t1d-run5b/48796901 \ | |
| t1d-run5b/48796903 \ | |
| t1d-run5b/48796902 \ | |
| t1d-run5b/49798101 \ | |
| t1d-run5b/49798102 \ | |
| t1d-run5b/49798103 \ | |
| t1d-run5b-redo/40612301 \ | |
| t1d-run5b-redo/40612302 \ | |
| t1d-run5b-redo/40612303 \ | |
| t1d-run5b-redo/40705901 \ | |
| t1d-run5b-redo/40705902 \ | |
| t1d-run5b-redo/40705904 \ | |
| t1d-run5b-redo/40761201 \ | |
| t1d-run5b-redo/40761202 \ | |
| t1d-run5b-redo/40761203 \ | |
| t1d-run5b-redo/40969901 \ | |
| t1d-run5b-redo/40969902 \ | |
| t1d-run5b-redo/40969904 \ | |
| t1d-run5b-redo/43131601 \ | |
| t1d-run5b-redo/43131602 \ | |
| t1d-run5b-redo/43131604 \ | |
| t1d-run5b-redo/45637601 \ | |
| t1d-run5b-redo/45637602 \ | |
| t1d-run5b-redo/45637604 \ | |
| t1d-run5b-redo/48796901 \ | |
| t1d-run5b-redo/48796902 \ | |
| t1d-run5b-redo/48796903 \ | |
| t1d-run5b-redo/49798101 \ | |
| t1d-run5b-redo/49798102 \ | |
| t1d-run5b-redo/49798103 \ | |
| t1d-run6a/40565601 \ | |
| t1d-run6a/40565602 \ | |
| t1d-run6a/40565603 \ | |
| t1d-run6a/41952301 \ | |
| t1d-run6a/41952302 \ | |
| t1d-run6a/41952303 \ | |
| t1d-run6a/42052001 \ | |
| t1d-run6a/42052002 \ | |
| t1d-run6a/42052004 \ | |
| t1d-run6a/44155001 \ | |
| t1d-run6a/44155002 \ | |
| t1d-run6a/44155004 \ | |
| t1d-run6a/46281901 \ | |
| t1d-run6a/46281902 \ | |
| t1d-run6a/46281904 \ | |
| t1d-run6a/46871801 \ | |
| t1d-run6a/46871802 \ | |
| t1d-run6a/46871803 \ | |
| t1d-run6a/46927301 \ | |
| t1d-run6a/46927302 \ | |
| t1d-run6a/46927304 \ | |
| t1d-run6a/48659901 \ | |
| t1d-run6a/48659902 \ | |
| t1d-run6a/48659903 \ | |
| t1d-run6b/42893101 \ | |
| t1d-run6b/42893102 \ | |
| t1d-run6b/42893104 \ | |
| t1d-run6b/44855301 \ | |
| t1d-run6b/44855302 \ | |
| t1d-run6b/44855304 \ | |
| t1d-run6b/45082401 \ | |
| t1d-run6b/45082402 \ | |
| t1d-run6b/45082404 \ | |
| t1d-run6b/46578401 \ | |
| t1d-run6b/46578402 \ | |
| t1d-run6b/46578403 \ | |
| t1d-run6b/46579201 \ | |
| t1d-run6b/46579202 \ | |
| t1d-run6b/46579203 \ | |
| t1d-run6b/47138101 \ | |
| t1d-run6b/47138102 \ | |
| t1d-run6b/47138104 \ | |
| t1d-run6b/47588601 \ | |
| t1d-run6b/47588602 \ | |
| t1d-run6b/47588604 \ | |
| t1d-run6b/48117301 \ | |
| t1d-run6b/48117302 \ | |
| t1d-run6b/48117304 \ | |
| t1d-run7a/40257001 \ | |
| t1d-run7a/40257002 \ | |
| t1d-run7a/40257003 \ | |
| t1d-run7a/41792501 \ | |
| t1d-run7a/41792502 \ | |
| t1d-run7a/41792503 \ | |
| t1d-run7a/43558001 \ | |
| t1d-run7a/43558002 \ | |
| t1d-run7a/43558003 \ | |
| t1d-run7a/45263801 \ | |
| t1d-run7a/45263802 \ | |
| t1d-run7a/45263803 \ | |
| t1d-run7a/45423101 \ | |
| t1d-run7a/45423102 \ | |
| t1d-run7a/45423103 \ | |
| t1d-run7a/47018001 \ | |
| t1d-run7a/47018002 \ | |
| t1d-run7a/47018003 \ | |
| t1d-run7a/48368201 \ | |
| t1d-run7a/48368202 \ | |
| t1d-run7a/48368204 \ | |
| t1d-run7a/49453101 \ | |
| t1d-run7a/49453102 \ | |
| t1d-run7a/49453103 \ | |
| t1d-run7b/40914201 \ | |
| t1d-run7b/40914202 \ | |
| t1d-run7b/40914203 \ | |
| t1d-run7b/42057801 \ | |
| t1d-run7b/42057802 \ | |
| t1d-run7b/42057803 \ | |
| t1d-run7b/42212501 \ | |
| t1d-run7b/42212502 \ | |
| t1d-run7b/42212503 \ | |
| t1d-run7b/43095901 \ | |
| t1d-run7b/43095902 \ | |
| t1d-run7b/43095904 \ | |
| t1d-run7b/46054101 \ | |
| t1d-run7b/46054102 \ | |
| t1d-run7b/46054104 \ | |
| t1d-run7b/48265001 \ | |
| t1d-run7b/48265002 \ | |
| t1d-run7b/48265003 \ | |
| t1d-run7b/48841901 \ | |
| t1d-run7b/48841902 \ | |
| t1d-run7b/48841903 \ | |
| t1d-run7b/49544901 \ | |
| t1d-run7b/49544902 \ | |
| t1d-run7b/49544903 \ | |
| t1d-run8a/41681701 \ | |
| t1d-run8a/41681702 \ | |
| t1d-run8a/41681704 \ | |
| t1d-run8a/43915401 \ | |
| t1d-run8a/43915402 \ | |
| t1d-run8a/43915403 \ | |
| t1d-run8a/44229701 \ | |
| t1d-run8a/44229702 \ | |
| t1d-run8a/44229703 \ | |
| t1d-run8a/44305301 \ | |
| t1d-run8a/44305302 \ | |
| t1d-run8a/44305304 \ | |
| t1d-run8a/45128901 \ | |
| t1d-run8a/45128902 \ | |
| t1d-run8a/45128903 \ | |
| t1d-run8a/45193801 \ | |
| t1d-run8a/45193802 \ | |
| t1d-run8a/45193803 \ | |
| t1d-run8a/45424201 \ | |
| t1d-run8a/45424202 \ | |
| t1d-run8a/45424203 \ | |
| t1d-run8a/45503301 \ | |
| t1d-run8a/45503302 \ | |
| t1d-run8a/45503304 \ | |
| t1d-run8b/40490901 \ | |
| t1d-run8b/40490902 \ | |
| t1d-run8b/40490904 \ | |
| t1d-run8b/41774101 \ | |
| t1d-run8b/41774102 \ | |
| t1d-run8b/41774104 \ | |
| t1d-run8b/41965901 \ | |
| t1d-run8b/41965902 \ | |
| t1d-run8b/41965904 \ | |
| t1d-run8b/42959901 \ | |
| t1d-run8b/42959902 \ | |
| t1d-run8b/42959904 \ | |
| t1d-run8b/45994301 \ | |
| t1d-run8b/45994302 \ | |
| t1d-run8b/45994303 \ | |
| t1d-run8b/47052401 \ | |
| t1d-run8b/47052402 \ | |
| t1d-run8b/47052403 \ | |
| t1d-run8b/47976601 \ | |
| t1d-run8b/47976602 \ | |
| t1d-run8b/47976604 \ | |
| t1d-run8b/48476501 \ | |
| t1d-run8b/48476502 \ | |
| t1d-run8b/48476504 \ | |
| t1d-run9a/42062701 \ | |
| t1d-run9a/42062702 \ | |
| t1d-run9a/42062703 \ | |
| t1d-run9a/42445001 \ | |
| t1d-run9a/42445002 \ | |
| t1d-run9a/42445003 \ | |
| t1d-run9a/43061901 \ | |
| t1d-run9a/43061902 \ | |
| t1d-run9a/43061903 \ | |
| t1d-run9a/43486101 \ | |
| t1d-run9a/43486102 \ | |
| t1d-run9a/43486104 \ | |
| t1d-run9a/43983801 \ | |
| t1d-run9a/43983802 \ | |
| t1d-run9a/43983803 \ | |
| t1d-run9a/45531401 \ | |
| t1d-run9a/45531402 \ | |
| t1d-run9a/45531403 \ | |
| t1d-run9a/47506301 \ | |
| t1d-run9a/47506302 \ | |
| t1d-run9a/47506303 \ | |
| t1d-run9a/49329901 \ | |
| t1d-run9a/49329902 \ | |
| t1d-run9a/49329904 \ | |
| t1d-run9b/42087701 \ | |
| t1d-run9b/42087702 \ | |
| t1d-run9b/42087703 \ | |
| t1d-run9b/42662801 \ | |
| t1d-run9b/42662802 \ | |
| t1d-run9b/42662803 \ | |
| t1d-run9b/42881001 \ | |
| t1d-run9b/42881002 \ | |
| t1d-run9b/42881003 \ | |
| t1d-run9b/45551601 \ | |
| t1d-run9b/45551602 \ | |
| t1d-run9b/45551603 \ | |
| t1d-run9b/45747901 \ | |
| t1d-run9b/45747902 \ | |
| t1d-run9b/45747903 \ | |
| t1d-run9b/45767701 \ | |
| t1d-run9b/45767702 \ | |
| t1d-run9b/45767703 \ | |
| t1d-run9b/45974701 \ | |
| t1d-run9b/45974702 \ | |
| t1d-run9b/45974704 \ | |
| t1d-run9b/48196401 \ | |
| t1d-run9b/48196402 \ | |
| t1d-run9b/48196403" | |
| export SAMPLES="t1d-run4a/45229504 \ | |
| t1d-run4a/45229501 \ | |
| t1d-run4a/45229502 \ | |
| t1d-run4a/40117104 \ | |
| t1d-run4a/40117101 \ | |
| t1d-run4a/40117102 \ | |
| t1d-run4a/42407802 \ | |
| t1d-run4a/42407801 \ | |
| t1d-run4a/42407804 \ | |
| t1d-run4a/45688804 \ | |
| t1d-run4a/45688801 \ | |
| t1d-run4a/45688802 \ | |
| t1d-run4a/49737804 \ | |
| t1d-run4a/49737802 \ | |
| t1d-run4a/49737801 \ | |
| t1d-run4a/46399402 \ | |
| t1d-run4a/46399404 \ | |
| t1d-run4a/46399401 \ | |
| t1d-run4a/49436402 \ | |
| t1d-run4a/49436403 \ | |
| t1d-run4a/49436401 \ | |
| t1d-run4a/47786201 \ | |
| t1d-run4a/47786202 \ | |
| t1d-run4a/47786203 \ | |
| t1d-run2a/40322601 \ | |
| t1d-run2a/40322602 \ | |
| t1d-run2a/40322604 \ | |
| t1d-run2a/40473801 \ | |
| t1d-run2a/40473802 \ | |
| t1d-run2a/40473803 \ | |
| t1d-run2a/41789801 \ | |
| t1d-run2a/41789802 \ | |
| t1d-run2a/41789803 \ | |
| t1d-run2a/42390801 \ | |
| t1d-run2a/42390802 \ | |
| t1d-run2a/42390803 \ | |
| t1d-run2a/43131301 \ | |
| t1d-run2a/43131302 \ | |
| t1d-run2a/43131303 \ | |
| t1d-run2a/43821501 \ | |
| t1d-run2a/43821502 \ | |
| t1d-run2a/43821503 \ | |
| t1d-run2a/48657801 \ | |
| t1d-run2a/48657902 \ | |
| t1d-run2a/48657903 \ | |
| t1d-run2a/48917101 \ | |
| t1d-run2a/48917102 \ | |
| t1d-run2a/48917104" | |
| ############################################################ | |
| # BWA MEM | |
| ############################################################ | |
| export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/fasta/human_g1k_v37.fasta | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1dra-bwamem | |
| for sample in `echo $SAMPLES`; | |
| do | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=6 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; bwa mem $GENOME fastq/${sample}_*_R1_*.fastq.gz fastq/${sample}_*_R2_*.fastq.gz -t 5 -M -R $'@RG\tID:$sample\tSM:$sample' | samtools view -Sb - > bam/$sample.bwamem.bam" | $QSUB | |
| done | |
| ############################################################ | |
| # SORT | |
| ############################################################ | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1dra-sort | |
| for sample in `echo $SAMPLES`; | |
| do | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=12000m:ncpus=8 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; samtools sort -@ 4 -m 2G bam/$sample.bwamem.bam bam/$sample.bwamem.sort" | $QSUB | |
| done | |
| ############################################################ | |
| # MARK DUPLICATES | |
| ############################################################ | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1d-dedup | |
| export BIN=/home/arq5x/cphg-home/shared/bin/picard-tools-1.72/ | |
| for sample in `echo $SAMPLES`; | |
| do | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=2 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; java -Xmx2g -jar $BIN/MarkDuplicates.jar \ | |
| INPUT=bam/$sample.bwamem.sort.bam \ | |
| OUTPUT=bam/$sample.bwamem.sort.dedup.bam \ | |
| TMP_DIR=$T1DHOME/bam \ | |
| VALIDATION_STRINGENCY=LENIENT \ | |
| ASSUME_SORTED=true \ | |
| METRICS_FILE=bam/$sample.markdup_metrics" | $QSUB; | |
| done | |
| ############################################################ | |
| # INDEX | |
| ############################################################ | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1d-idx | |
| for sample in `echo $SAMPLES`; | |
| do | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=1000m:ncpus=1 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; samtools index bam/$sample.bwamem.sort.dedup.bam" | $QSUB | |
| done | |
| ############################################################ | |
| # COVERAGE | |
| ############################################################ | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1d-cov | |
| for sample in `echo $SAMPLES`; | |
| do | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=2000m:ncpus=1 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; rm coverage/$sample.cov.txt; bedtools coverage -hist -abam bam/$sample.bwamem.sort.bam -b bed/targets.bed > coverage/$sample.cov.txt" | $QSUB | |
| done | |
| ############################################################ | |
| # MERGE BAMS | |
| ############################################################ | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1d-merge | |
| export BIN=/home/arq5x/cphg-home/shared/bin/picard-tools-1.60 | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=4 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; java -Xmx4g -jar $BIN/MergeSamFiles.jar \ | |
| O=bam/all.bwamem.sort.dedup.20140822.bam \ | |
| I=bam/ra-run10/217.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/218.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/219.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/220.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/221.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/222.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/223.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/224.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/225.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/226.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/227.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/228.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/229.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/230.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/231.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/232.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/233.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/234.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/235.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/236.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/237.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/238.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/239.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run10/240.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/1.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/10.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/11.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/12.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/241.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/242.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/243.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/244.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/245.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/246.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/247.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/248.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/249.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/250.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/251.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/252.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/253.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/254.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/255.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/256.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/257.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/258.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/259.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/260.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/261.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/262.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/263.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run11/264.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/13.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/14.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/15.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/16.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/17.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/18.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/19.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/2.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/20.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/21.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/22.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/265.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/266.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/267.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/268.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/269.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/270.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/271.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/272.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/273.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/274.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/275.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/276.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/277.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/278.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/279.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/280.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/281.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/282.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/283.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/284.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/285.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/286.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/287.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run12/288.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/23.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/24.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/3.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/289.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/290.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/291.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/292.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/293.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/294.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/295.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/296.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/297.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/298.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/299.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/300.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/301.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/302.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/303.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/304.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/305.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/306.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/307.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/308.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/309.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/310.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/311.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run13/312.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/4.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/313.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/314.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/315.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/316.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/317.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/318.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/319.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/320.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/321.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/322.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/323.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/324.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/325.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/326.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/327.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/328.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/329.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/330.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/331.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/332.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/333.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/334.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/335.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run14/336.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/5.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/337.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/338.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/339.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/340.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/341.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/342.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/343.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/344.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/345.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/346.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/347.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/348.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/349.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/350.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/351.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/352.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/353.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/354.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/355.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/356.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/357.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/358.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/359.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run15/360.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/6.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/361.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/362.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/363.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/364.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/365.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/366.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/367.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/368.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/369.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/370.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/371.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/372.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/373.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/374.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/375.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/376.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/377.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/378.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/379.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/380.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/381.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/382.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/383.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run16/384.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/7.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/8.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run1/9.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/25.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/26.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/27.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/28.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/29.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/30.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/31.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/32.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/33.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/34.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/35.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/36.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/37.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/38.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/39.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/40.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/41.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/42.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/43.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/44.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/45.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/46.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/47.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run2/48.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/49.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/50.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/51.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/52.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/53.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/54.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/55.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/56.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/57.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/58.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/59.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/60.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/61.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/62.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/63.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/64.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/65.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/66.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/67.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/68.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/69.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/70.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/71.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run3/72.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/73.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/74.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/75.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/76.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/77.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/78.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/79.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/80.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/81.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/82.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/83.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/84.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/85.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/86.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/87.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/88.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/89.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/90.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/91.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/92.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/93.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/94.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/95.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run4/96.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/100.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/101.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/102.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/103.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/104.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/105.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/106.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/107.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/108.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/145.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/146.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/147.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/148.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/149.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/150.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/151.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/152.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/153.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/154.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/155.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/156.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/97.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/98.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run5/99.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/109.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/110.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/111.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/112.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/113.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/114.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/115.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/116.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/117.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/118.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/119.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/120.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/121.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/122.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/123.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/124.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/125.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/126.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/127.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/128.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/129.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/130.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/131.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run6/132.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/133.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/134.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/135.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/136.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/137.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/138.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/139.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/140.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/141.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/142.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/143.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/144.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/157.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/158.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/159.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/160.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/161.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/162.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/163.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/164.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/165.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/166.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/167.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run7/168.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/169.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/170.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/171.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/172.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/173.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/174.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/175.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/176.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/177.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/178.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/179.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/180.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/181.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/182.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/183.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/184.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/185.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/186.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/187.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/188.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/189.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/190.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/191.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run8/192.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/193.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/194.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/195.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/196.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/197.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/198.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/199.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/200.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/201.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/202.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/203.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/204.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/205.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/206.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/207.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/208.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/209.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/210.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/211.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/212.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/213.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/214.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/215.bwamem.sort.dedup.bam \ | |
| I=bam/ra-run9/216.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42192101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42192102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42192104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42552101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42552102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42552104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42933801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42933802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/42933804.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/45994201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/45994202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/45994203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/46197301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/46197302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/46197304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/47956601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/47956602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/47956603.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/48219501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/48219502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/48219503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/48515001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/48515002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10a/48515003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/40010401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/40010402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/40010404.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/41245501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/41245502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/41245504.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/43266601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/43266602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/43266604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/44181401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/44181402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/44181403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45158201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45158202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45158203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45320801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45320802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45320804.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45541601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45541602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45541604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45925501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45925502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run10b/45925503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/40983201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/40983202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/40983204.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44005001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44005002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44005003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44495201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44495202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44495203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44997901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44997902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/44997904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/45383001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/45383002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/45383004.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/46966301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/46966302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/46966303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/47585201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/47585202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/47585203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/47789101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/47789102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run11/47789103.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/41032601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/41032602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/41032603.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/42044401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/42044402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/42044403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44003301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44003302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44003304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44123901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44123902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44123903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44143001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44143002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/44143004.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/46628201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/46628202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/46628204.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/47960801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/47960802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/47960803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/48094101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/48094102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1/48094104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/41032601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/41032602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/41032603.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/42044401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/42044402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/42044403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44003301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44003302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44003304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44123901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44123902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44123903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44143001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44143002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/44143004.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/46628201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/46628202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/46628204.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/47960801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/47960802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/47960803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/48094101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/48094102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run1-v3/48094104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/40322601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/40322602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/40322604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/40473801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/40473802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/40473803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/41789801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/41789802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/41789803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/42390801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/42390802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/42390803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/43131301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/43131302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/43131303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/43821501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/43821502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/43821503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/48657801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/48657902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/48657903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/48917101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/48917102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a/48917104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/40322601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/40322602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/40322604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/40473801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/40473802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/40473803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/41789801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/41789802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/41789803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/42390801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/42390802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/42390803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/43131301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/43131302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/43131303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/43821501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/43821502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/43821503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/48657901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/48657902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/48657903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/48917101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/48917102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2a-redo/48917104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/41050801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/41050802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/41050803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/43293801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/43293802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/43293804.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/44213301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/44213302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/44213303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/44724901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/44724902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/44724903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/45676501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/45676502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/45676504.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/45808601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/45808602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/45808604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/46291001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/46291002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/46291003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/47439601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/47439602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run2b/47439604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/40458101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/40458102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/40458103.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/41073901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/41073902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/41073903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/41075701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/41075702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/41075704.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/42153401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/42153402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/42153404.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/43673001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/43673002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/43673003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/44270401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/44270402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/44270404.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/44638201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/44638202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/44638203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/45789703.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/46789701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3a/46789702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/40946401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/40946402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/40946403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/42448401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/42448402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/42448403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/44609801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/44609802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/44609803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/45432701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/45432702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/45432703.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47076101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47076102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47076103.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47203001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47203002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47203003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47384401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47384402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/47384404.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/49699501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/49699502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run3b/49699503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/40117101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/40117102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/40117104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/42407801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/42407802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/42407804.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/45229501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/45229502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/45229504.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/45688801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/45688802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/45688804.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/46399401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/46399402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/46399404.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/47786201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/47786202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/47786203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/49436401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/49436402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/49436403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/49737801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/49737802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4a/49737804.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/41209801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/41209802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/41209804.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/42239101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/42239102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/42239104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/47791201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/47791202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/47791203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/48842701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/48842702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/48842704.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49423501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49423502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49423503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49484401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49484402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49484404.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49530101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49530102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49530104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49713901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49713902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run4b/49713904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/40203301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/40203302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/40203307.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/40712001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/40712002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/40712003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/42545801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/42545802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/42545803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/43199001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/43199002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/43199003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/44194701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/44194702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/44194703.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/44673501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/44673502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/44673507.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/47948201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/47948202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/47948203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/49055901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/49055902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5a/49055903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40612302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40612301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40612303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40705901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40705902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40705904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40761201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40761202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40761203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40969901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40969902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/40969904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/43131601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/43131602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/43131604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/45637601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/45637602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/45637604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/48796901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/48796903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/48796902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/49798101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/49798102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b/49798103.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40612301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40612302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40612303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40705901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40705902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40705904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40761201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40761202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40761203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40969901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40969902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/40969904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/43131601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/43131602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/43131604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/45637601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/45637602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/45637604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/48796901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/48796902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/48796903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/49798101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/49798102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run5b-redo/49798103.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/40565601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/40565602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/40565603.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/41952301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/41952302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/41952303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/42052001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/42052002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/42052004.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/44155001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/44155002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/44155004.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46281901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46281902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46281904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46871801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46871802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46871803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46927301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46927302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/46927304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/48659901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/48659902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6a/48659903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/42893101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/42893102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/42893104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/44855301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/44855302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/44855304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/45082401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/45082402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/45082404.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/46578401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/46578402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/46578403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/46579201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/46579202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/46579203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/47138101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/47138102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/47138104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/47588601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/47588602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/47588604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/48117301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/48117302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run6b/48117304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/40257001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/40257002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/40257003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/41792501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/41792502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/41792503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/43558001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/43558002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/43558003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/45263801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/45263802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/45263803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/45423101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/45423102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/45423103.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/47018001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/47018002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/47018003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/48368201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/48368202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/48368204.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/49453101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/49453102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7a/49453103.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/40914201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/40914202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/40914203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/42057801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/42057802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/42057803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/42212501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/42212502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/42212503.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/43095901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/43095902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/43095904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/46054101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/46054102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/46054104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/48265001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/48265002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/48265003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/48841901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/48841902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/48841903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/49544901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/49544902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run7b/49544903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/41681701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/41681702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/41681704.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/43915401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/43915402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/43915403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/44229701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/44229702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/44229703.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/44305301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/44305302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/44305304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45128901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45128902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45128903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45193801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45193802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45193803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45424201.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45424202.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45424203.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45503301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45503302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8a/45503304.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/40490901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/40490902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/40490904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/41774101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/41774102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/41774104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/41965901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/41965902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/41965904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/42959901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/42959902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/42959904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/45994301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/45994302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/45994303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/47052401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/47052402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/47052403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/47976601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/47976602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/47976604.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/48476501.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/48476502.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run8b/48476504.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/42062701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/42062702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/42062703.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/42445001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/42445002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/42445003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43061901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43061902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43061903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43486101.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43486102.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43486104.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43983801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43983802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/43983803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/45531401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/45531402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/45531403.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/47506301.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/47506302.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/47506303.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/49329901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/49329902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9a/49329904.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42087701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42087702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42087703.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42662801.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42662802.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42662803.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42881001.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42881002.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/42881003.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45551601.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45551602.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45551603.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45747901.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45747902.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45747903.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45767701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45767702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45767703.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45974701.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45974702.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/45974704.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/48196401.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/48196402.bwamem.sort.dedup.bam \ | |
| I=bam/t1d-run9b/48196403.bwamem.sort.dedup.bam \ | |
| TMP_DIR=$T1DHOME/bam \ | |
| VALIDATION_STRINGENCY=SILENT \ | |
| USE_THREADING=true" | $QSUB; | |
| ############################################################ | |
| # Call SNPs and INDELs with GATK W/O using BAQ. | |
| ############################################################ | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1d-varbaq | |
| export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/fasta/human_g1k_v37.fasta | |
| export BIN=/home/arq5x/cphg-home/shared/bin/GenomeAnalysisTK-2.4-9-g532efad/ | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=16000m:ncpus=24 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; java -Xmx4g -jar $BIN/GenomeAnalysisTK.jar \ | |
| -T UnifiedGenotyper \ | |
| -glm BOTH \ | |
| --num_threads 20 \ | |
| -baq OFF \ | |
| -R $GENOME \ | |
| --filter_mismatching_base_and_quals \ | |
| -I bam/all.bwamem.sort.dedup.20140822.bam \ | |
| -o varcalling/all.raw.nobaq.20140822.vcf" | $QSUB; | |
| ############################################################ | |
| # VQSR | |
| ############################################################ | |
| # http://www.broadinstitute.org/gatk/guide/article?id=1259 | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1d-vqsr | |
| export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/fasta/human_g1k_v37.fasta | |
| export BIN=/home/arq5x/cphg-home/shared/bin/GenomeAnalysisTK-2.4-9-g532efad/ | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=16000m:ncpus=6 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; java -Xmx4g -jar $BIN/GenomeAnalysisTK.jar \ | |
| -T VariantRecalibrator \ | |
| -R $GENOME \ | |
| --num_threads 4 \ | |
| -input varcalling/all.raw.nobaq.vcf \ | |
| -recalFile varcalling/all.raw.nobaq.vcf.output.recal \ | |
| -tranchesFile varcalling/all.raw.nobaq.vcf.output.tranches \ | |
| -resource:hapmap,known=false,training=true,truth=true,prior=15.0 gatk-resources/hapmap_3.3.b37.vcf \ | |
| -resource:omni,known=false,training=true,truth=true,prior=12.0 gatk-resources/1000G_omni2.5.b37.vcf \ | |
| -resource:1000G,known=false,training=true,truth=false,prior=10.0 gatk-resources/1000G_phase1.snps.high_confidence.b37.vcf \ | |
| -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 gatk-resources/dbsnp_138.b37.vcf \ | |
| -an QD -an MQRankSum -an ReadPosRankSum -an FS -an DP \ | |
| -mode SNP " | $QSUB; | |
| ############################################################ | |
| # Apply VQSR | |
| ############################################################ | |
| export T1DHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq | |
| export STEPNAME=t1d-vqsra | |
| export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/fasta/human_g1k_v37.fasta | |
| export BIN=/home/arq5x/cphg-home/shared/bin/GenomeAnalysisTK-2.4-9-g532efad/ | |
| export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=16000m:ncpus=16 -N $STEPNAME -m bea -M arq5x@virginia.edu"; | |
| echo "cd $T1DHOME; java -Xmx4g -jar $BIN/GenomeAnalysisTK.jar \ | |
| -T ApplyRecalibration \ | |
| -R $GENOME \ | |
| --num_threads 4 \ | |
| -input varcalling/all.raw.nobaq.vcf \ | |
| -o varcalling/all.raw.nobaq.vqsr.vcf \ | |
| -recalFile varcalling/all.raw.nobaq.vcf.output.recal \ | |
| -tranchesFile varcalling/all.raw.nobaq.vcf.output.tranches \ | |
| -mode SNP \ | |
| --ts_filter_level 99.0" | $QSUB | |
| ############################################################ | |
| # snpEff | |
| ############################################################ | |
| java -Xmx4g -jar snpEff.jar eff -v GRCh37.69 /home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/varcalling/all.raw.nobaq.vqsr.vcf \ | |
| > /home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/varcalling/all.raw.nobaq.vqsr.snpEff.vcf | |
| bgzip all.raw.nobaq.vqsr.snpEff.vcf | |
| # move to laptop | |
| cd /Users/arq5x/Documents/Projects/QuinlanLab/Collaboration/T1D-RA-H3K4me3-Seq/vcf/72-samples | |
| scp fir.itc.virginia.edu:/home/arq5x/cphg-home/cphg-quinlan/projects/t1d-ra-funcseq/varcalling/all.raw.nobaq.vqsr.snpEff.vcf.gz . | |
| gemini load -v all.raw.nobaq.vqsr.snpEff.vcf.gz -t snpEff --cores 4 t1d-ra.72samples.vqsr.db | |
| gemini annotate -a boolean -f ../../targets.chr.slop300.bed.gz -c on_target_300 t1d-ra.72samples.vqsr.db | |
| ############################################################ | |
| # TO DO | |
| ############################################################ | |
| 1. run the V3 coverage analysis. | |
| 2. get VQSR and quality metrics in the file. | |
| 3. need genotypes for each sample. |
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