allele information from samtools mpileup contents

[fatakias]

Dear all,

I need help with allele information from samtools mpileup contents

I have the following workflow for diagnostics:

samtools view -b whole_exome.sorted.bam chr2:12345678-32345678 > zoom_region.bam
samtools mpileup -f ref.fa -B -q 1 -Q 30 -SD zoom_region.bam > info.mpileup.txt

The subsequent info.mpileup.txt has information as described in

http://samtools.sourceforge.net/pileup.shtml

Is there a script or automated method that can parse the allele info: #A, T, G, C .. from the mpileup / pileup information of the original bam file. I need to repeat this for many base positions, hence the need to automate it. Hope you can please help. Would appreciate any help / pointers.

Thanks in advance,
Best,
sarosh

[dnusol]

dear Sarosh,

did you manage to get the per base ACGT count in any way?

best,

Dave

[swbarnes2]

Why not use bcftools to make a vcf, instead of a pileup file?

Then if you want, filter the vcf with bedtools and a bedfile of your candidate regions.