Tutorial: Piping With Samtools, Bwa And Bedtools

In this tutorial I will introduce some concepts related to unix piping. Piping is a very useful feature to avoid creation of intermediate use once files. It is assumed that bedtools, samtools, and bwa are installed. Lets begin with a typical command to do paired end mapping with bwa: (./ means look in current directory only)#-t 4 is for using 4 threads/cores bwa aln -t 4 ./hg19.fasta ./s1_1.fastq > ./s1_1.sai bwa aln -t 4 ./hg19.fasta ./s1_2.fastq > ./s1_2.sai bwa sampe ./hg19.fasta ./s1_1.sai ./s1_2.sai ./s1_1.fastq ./s1_2.fastq > s1.sam Supposed we wish to compress sam to bam, sort, remove duplicates, and create a bed file.samtools view -Shu s1.sam > s1.bam samtools sort s1.bam s1_sorted samtools rmdup -s s1_sorted.bam s1_sorted_nodup.bam bamToBed -i s1_sorted_nodup.bam > s1_sorted_nodup.bed This workflow above creates many files that are only used once (such as s1.bam) and we can use the unix pipe utility to reduce the number intermediate files created. The pipe function is the character | and what it does is ta ...