I would like to get the counts of A/C/G/T high quality bases aligned at each position from a bam file.
I know that 'samtools mpileup' gives a string with actual read bases and their quality scores ("reads" and "quals" in example below). So, yes I can parse it. But is there a ready-made option for this?
I also know that the '-u' option gives something similar in the I16 filed (number of bases in forward and reverse strand which are ref or non-ref) but not quite the full A/C/G/T count.
So, is parsing each mpileup line my only option? (Are there other programs, say picard, which might be better suited for this?)
Thanks,
Gulu
I know that 'samtools mpileup' gives a string with actual read bases and their quality scores ("reads" and "quals" in example below). So, yes I can parse it. But is there a ready-made option for this?
Code:
Chr pos Ref Dep Reads Quals 1 3000016 A 5 ..C.^~. /<%A?
So, is parsing each mpileup line my only option? (Are there other programs, say picard, which might be better suited for this?)
Thanks,
Gulu