Hi all,
I want to get basic information regarding variant calling in a vcf format - in term of general coverage at each base as well as every allele coverage at each bas.
Running samtools' mpileup doesn't give the "AC" (allele count) attribute I need.
I find it hard to believe that mpileup give a lot of statistics for each base, but doesn't supply a raw count of each allele.
What am I missing?
Thanks!
Rachelly.
I want to get basic information regarding variant calling in a vcf format - in term of general coverage at each base as well as every allele coverage at each bas.
Running samtools' mpileup doesn't give the "AC" (allele count) attribute I need.
I find it hard to believe that mpileup give a lot of statistics for each base, but doesn't supply a raw count of each allele.
What am I missing?
Thanks!
Rachelly.
