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Bedtools protocols.
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| # /home/arq5x/cphg-home/projects/bedtools-curr-prot-bx | |
| ####################################################### | |
| # 1. Create subsamples of BAM file and convert to BED. | |
| ####################################################### | |
| bedtools bamtobed -i ~/cphg-quinlan/projects/rs-exome/bam/1478PC0009B.conc.on.pos.bam | \ | |
| cut -f 1-3 \ | |
| > datasets/sample.100M.bam.bed & | |
| samtools view -us 0.10 ~/cphg-quinlan/projects/rs-exome/bam/1478PC0009B.conc.on.pos.bam | \ | |
| bedtools bamtobed -i - | \ | |
| cut -f 1-3 \ | |
| > datasets/sample.10M.bam.bed & | |
| samtools view -us 0.01 ~/cphg-quinlan/projects/rs-exome/bam/1478PC0009B.conc.on.pos.bam | \ | |
| bedtools bamtobed -i - | \ | |
| cut -f 1-3 \ | |
| > datasets/sample.1M.bam.bed & | |
| ####################################################### | |
| # 2. Collect run times for 2.16, 2.17, 2.18, and bedops | |
| ####################################################### | |
| pwd | |
| /if2/arq5x/cphg-quinlan/projects/bedtools-curr-prot-bx | |
| # bedtools2 -sorted (bedtools-s) | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.10K.bam.bed -c -sorted > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.100K.bam.bed -c -sorted > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.1M.bam.bed -c -sorted > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.10M.bam.bed -c -sorted > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.100M.bam.bed -c -sorted > /dev/null | |
| # bedtools2 (bedtools-u) | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.10K.bam.bed -c > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.100K.bam.bed -c > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.1M.bam.bed -c > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.10M.bam.bed -c > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedtools intersect -a datasets/ccds.exons.bed -b datasets/sample.100M.bam.bed -c > /dev/null | |
| # bedmap (bedmap) | |
| # bedmap requires sort -k1,1 -k2,2n -k3,3n | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.10K.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.100K.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.1M.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.10M.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.100M.bam.bedmap.bed > /dev/null | |
| # bedmap with error checking (bedmap-e | |
| # bedmap requires sort-bed | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --ec --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.10K.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --ec --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.100K.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --ec --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.1M.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --ec --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.10M.bam.bedmap.bed > /dev/null | |
| /if2/arq5x/cphg-quinlan/shared/bin/runit /if2/arq5x/cphg-quinlan/shared/bin/bedmap --ec --echo --count --bp-ovr 1 datasets/ccds.exons.bedmap.bed datasets/sample.100M.bam.bedmap.bed > /dev/null | |
| tool time mem size | |
| bedtools-s 0.65 2.2 1e4 | |
| bedtools-s 0.86 2.2 1e5 | |
| bedtools-s 1.25 2.2 1e6 | |
| bedtools-s 5.30 3.5 1e7 | |
| bedtools-s 47.81 15.9 1e8 | |
| bedtools-u 0.87 13.5 1e4 | |
| bedtools-u 1.06 52.1 1e5 | |
| bedtools-u 2.06 454.0 1e6 | |
| bedtools-u 13.6 44042.2 1e7 | |
| bedtools-u NA NA 1e8 | |
| bedops 0.81 1.8 1e4 | |
| bedops 0.95 2.6 1e5 | |
| bedops 1.32 2.8 1e6 | |
| bedops 6.26 3.2 1e7 | |
| bedops 60.69 6.00 1e8 | |
| bedops-e 1.13 0.8 1e4 | |
| bedops-e 1.39 0.8 1e5 | |
| bedops-e 2.62 0.9 1e6 | |
| bedops-e 16.05 1.2 1e7 | |
| bedops-e 164.18 7.9 1e8 | |
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| setwd('/Users/arq5x/Documents/Career/QuinlanArticles/2014/bedtools_curr_protocols_bx/protocols/speed') | |
| library(ggplot2) | |
| theme_set(theme_bw(18)) | |
| tool_comparo <- read.table("speed-comparo.txt",header=TRUE) | |
| bts <- subset(tool_comparo, tool %in% c("bedtools-s")) | |
| btu <- subset(tool_comparo, tool %in% c("bedtools-u")) | |
| bor <- subset(tool_comparo, tool %in% c("bedops")) | |
| boe <- subset(tool_comparo, tool %in% c("bedops-e")) | |
| plot(bts[,4], bts[,2], xaxt = "n", yaxt="n", | |
| log="x", 'b', col="darkred", | |
| lwd=3, ylim=c(0,180), | |
| xlab="Number of BAM alignments", | |
| ylab="Time in seconds") | |
| points(btu[,4], btu[,2], xaxt = "n", 'b', col="darkred", lwd=3, lty=3) | |
| points(bor[,4], bor[,2], xaxt = "n", 'b', col="darkgray", lwd=3) | |
| points(boe[,4], boe[,2], xaxt = "n", 'b', col="darkgray", lwd=3, lty=3) | |
| axis(2, at=c(0,10,20,40,60,120,180), labels=c(0,10,20,40,60,120,180)) | |
| axis(1, at=c(1e4,1e5,1e6,1e7,1e8), labels=c("1e4","1e5","1e6","1e7","1e8")) | |
| # add a legend. | |
| legend('topleft', c("bedtools (sorted)","bedtools (unsorted)", "bedops", "bedops w/ error checking"), | |
| lwd=c(3,3,3,3), lty=c(1,3,1,3), col=c('darkred', 'darkred', 'darkgray', 'darkgray'), bty='n') | |
| # memory plot | |
| plot(bts[,4], log10(bts[,3]), xaxt = "n", yaxt="n", | |
| log="x", 'b', col="darkred", | |
| lwd=3, ylim=c(0,6), | |
| xlab="Number of BAM alignments", | |
| ylab="RAM") | |
| points(btu[,4], log10(btu[,3]), xaxt = "n", 'b', col="darkred", lwd=3, lty=3) | |
| points(bor[,4], log10(bor[,3]), xaxt = "n", 'b', col="darkgray", lwd=3) | |
| points(boe[,4], log10(boe[,3]), xaxt = "n", 'b', col="darkgray", lwd=3, lty=3) | |
| axis(2, at=c(0,1,2,3,4,5), labels=c(0,"10Mb","100Mb","1Gb","10Gb","100Gb")) | |
| axis(1, at=c(1e4,1e5,1e6,1e7,1e8), labels=c("1e4","1e5","1e6","1e7","1e8")) | |
| # add a legend. | |
| legend('topleft', c("bedtools (sorted)","bedtools (unsorted)", "bedops", "bedops w/ error checking"), | |
| lwd=c(3,3,3,3), lty=c(1,3,1,3), col=c('darkred', 'darkred', 'darkgray', 'darkgray'), bty='n') |
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