Question: Mutect Allele Counts Vs Mpileup
gravatar for Noushin N
6.9 years ago by
Noushin N580
Baltimore, MD
Noushin N580 wrote:

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>>@;=


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!

mpileup • 3.1k views
ADD COMMENTlink modified 6.8 years ago by enabieva50 • written 6.9 years ago by Noushin N580

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 !



ADD REPLYlink written 6.0 years ago by Chirag Nepal2.3k

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.


ADD REPLYlink written 5.9 years ago by Noushin N580
gravatar for enabieva
6.8 years ago by
enabieva50 wrote:

Hi, having had a similar problem, I just discovered the answer on page 1 of Supplementary Materials of the MuTect paper (among other things it filters on total baq scores of all mismatches in the read). Hope that helps.

ADD COMMENTlink written 6.8 years ago by enabieva50

Thank you so much! That is most likely the reason.

ADD REPLYlink written 6.8 years ago by Noushin N580
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