I used Mutect to call somatic mutations in my exome sequencing experiment. Just to validate some results, I decided to make mpileup at the positions of somatic mutations. However, I am finding some discrepancies in the number of read counts supporting the alleles at some positions, between mpileup results and what mutect reports in its "t_ref_count" and "t_alt_count" columns in the output.
I do realize that some quality filter is applied to the reads. However, I do not seem to find the value mutect uses by default. Turning to my mpileup file, I have tried filtering at different thresholds of mapping quality; but none seem to result in the values reported by mutect.
Here are two example lines:
mpileup: chr11 3075562 t 29 ..c,cc,,,,C.,c,C,,,.,c,,..,,. #>!@!!?@@?!?@!?!:>@??!@6>>@;=
chrom start end ref alt t_ref_count t_alt_count n_ref_count n_alt_count
chr11 3075561 3075562 T C 20 5 25 0
All the bases reporting "c" seem to have mapping quality of zero, which is the minimum quality at this position. So, any filtering will result in t_alt_count of 0.
Is there anyway to find a compromise between the counts from the two sources?