Hi everyone,
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>>@;=
mutect:
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?
Thank you!
Hi Noushin,
I have a similar question like you, would be nice if you could help.
I have muTect output, and wanted to see the read count for each variant.
contig position context ref_allele alt_allele t_ref_count t_alt_count t_ref_sum t_alt_sum t_ref_max_mapq t_alt_max_mapq t_ins_count t_del_count normal_best_gt init_n_lod n_ref_count n_alt_count n_ref_sum n_alt_sum judgement
chr1 22328092 CCAxTCA A G 22 4 636 103 -2 59 0 0 AA 8.123008 27 0 803 0 KEEP
chr1 117142707 GGCxGAC G A 32 12 760 334 124 89 0 0 GG 7.743379 26 0 612 0 KEEP
I see that, t_ref_count and t_alt_count do not sum up to t_ref_sum. Same applies for normal.
Could you explain why is that.
Thanks !
Hi Chriag,
I came back to biostars today after a long while and noticed this comment. You probably have this figured out already, but I am adding this for future reference.
According to documentation, t_ref_count, and t_alt_count report the read counts suporting each allele, while t_ref_sum, and t_alt_sum correspond to the sum of read quality scores.
Best,
Noushin