Get the readcounts at a locus in a strand specific manner by piping samtools mpileup output. This program has been tested on samtools v1.6
git clone git@github.com:kriemo/mpileup2readcounts
cd mpileup2readcounts
makesamtools mpileup \
-f ref.fa \
-l regions.bed \
alignments.bam \
| mpileupToReadCounts
## only report positions with depth >= 5 reads
samtools mpileup \
-f ref.fa \
-l regions.bed \
alignments.bam \
| mpileupToReadCounts -d 5
## only report positions with depth >= 5 reads
## report complement positions (useful for strand-specific fr-firststranded libraries)
samtools mpileup \
-f ref.fa \
-l regions.bed \
alignments.bam \
| mpileupToReadCounts -d 5 -rchr pos strand depth ref_base refcount acount ccount gcount tcount ncount mmcount delcount inscount
chr1 10004 - 8 G 8 0 0 8 0 0 0 0 0
chr1 10005 - 10 G 10 0 0 10 0 0 0 0 0
chr1 10006 - 12 G 12 0 0 12 0 0 0 0 0
chr1 10007 - 13 A 13 13 0 0 0 0 0 0 0
chr1 10008 - 11 T 10 1 0 0 10 0 1 0 0
chr1 10009 - 11 T 11 0 0 0 11 0 0 0 0
chr1 10010 - 22 G 22 0 0 22 0 0 0 0 0
chr1 10011 - 23 G 23 0 0 23 0 0 0 0 0
chr1 10012 - 25 G 25 0 0 25 0 0 0 0 0
chr1 10013 - 26 A 26 26 0 0 0 0 0 0 0
chr1 10014 - 22 T 22 0 0 0 22 0 0 0 0
chr1 10015 - 24 T 24 0 0 0 24 0 0 0 0
with -r set
chr pos strand depth ref_base refcount acount ccount gcount tcount ncount mmcount delcount inscount
chr1 10004 + 8 C 8 0 8 0 0 0 0 0 0
chr1 10005 + 10 C 10 0 10 0 0 0 0 0 0
chr1 10006 + 12 C 12 0 12 0 0 0 0 0 0
chr1 10007 + 13 T 13 0 0 0 13 0 0 0 0
chr1 10008 + 10 A 10 10 0 0 0 0 0 0 0
chr1 10009 + 11 A 11 11 0 0 0 0 0 0 0
chr1 10010 + 22 C 22 0 22 0 0 0 0 0 0
chr1 10011 + 23 C 23 0 23 0 0 0 0 0 0
chr1 10012 + 25 C 25 0 25 0 0 0 0 0 0
chr1 10013 + 26 T 26 0 0 0 26 0 0 0 0
chr1 10014 + 22 A 22 22 0 0 0 0 0 0 0
chr1 10015 + 24 A 24 24 0 0 0 0 0 0 0
chr1 10016 + 30 C 30 0 30 0 0 0 0 0 0
chr1 10016 - 6 G 6 0 0 6 0 0 0 0 0
chr1 10017 + 29 C 29 0 29 0 0 0 0 0 0
chr1 10017 - 7 G 7 0 0 7 0 0 0 0 0
chr1 10018 + 32 C 32 0 32 0 0 0 0 0 0