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arq5x/AFS_analysis_for_311_samples.ipynb

Last active January 2, 2016 01:39
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T1D-RA targeted regulatory sequencing
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AFS_analysis_for_311_samples.ipynb
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Raw
comparison-to-immunochip.sh
# /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 $0"\tunmapped"}}' unmapped) | sort -k4,4n > lifted.bed
paste t1d-ra.exp.ontarget.hg19.bed3 lifted.bed > full
paste t1d-ra.exp.ontarget.hg19.bed full > t1d-ra.exp.ontarget.hg19.and.hg18.bed
Raw
coverage-analysis.R
args <- commandArgs(TRUE)
# Get a list of the bedtools output files you'd like to read in
print(files <- list.files(pattern="cov.genomewide.txt$"))
# 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))
Raw
make-coverage-plots
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
Raw
qc-questions.md
  1. Duplication rate
  2. Coverage per target w/ w/o duplicates
  3. Number of novel variants
  4. AFS
Raw
workflow.sh
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 \
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ra-run10/240 \
ra-run1/1 \
ra-run1/10 \
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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 \
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ra-run1/16 \
ra-run1/17 \
ra-run1/18 \
ra-run1/19 \
ra-run1/2 \
ra-run1/20 \
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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 \
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ra-run12/281 \
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ra-run1/23 \
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ra-run1/3 \
ra-run13/289 \
ra-run13/290 \
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ra-run8/169 \
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ra-run8/172 \
ra-run8/173 \
ra-run8/174 \
ra-run8/175 \
ra-run8/176 \
ra-run8/177 \
ra-run8/178 \
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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 \
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ra-run9/201 \
ra-run9/202 \
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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 \
t1d-run10b/41245502 \
t1d-run10b/41245504 \
t1d-run10b/43266601 \
t1d-run10b/43266602 \
t1d-run10b/43266604 \
t1d-run10b/44181401 \
t1d-run10b/44181402 \
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 \
t1d-run1-v3/44003304 \
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 [email protected]";
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 [email protected]";
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 [email protected]";
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 [email protected]";
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 [email protected]";
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 [email protected]";
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 \
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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 [email protected]";
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 [email protected]";
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 [email protected]";
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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