Awesome

Synopsis

Get the readcounts at a locus by piping samtools mpileup output. This allows us to be flexible with the version of samtools used. This program has been tested on samtools v1.1

Install

mkdir build
cd build
cmake ..
make

Usage

samtools mpileup -f ref.fa -l regions.bed alignments.bam | mpileup2readcounts sample1

##Example output

chr        pos        depth      ref_base           refcount           altcount           acount     ccount     gcount     tcount     ncount     indelcount         identifier
1          10205      3          A          3          0          3          0          0          0          0          0          sample1
1          10206      3          A          3          0          3          0          0          0          0          0          sample1
1          10207      4          C          4          0          0          4          0          0          0          0          sample1
1          10208      4          C          4          0          0          4          0          0          0          0          sample1
1          10209      4          C          4          0          0          4          0          0          0          0          sample1
1          10210      4          T          4          0          0          0          0          4          0          0          sample1
1          10211      4          A          4          0          4          0          0          0          0          0          sample1
1          10212      3          A          3          0          3          0          0          0          0          0          sample1
1          10213      4          C          4          0          0          4          0          0          0          0          sample1