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Why t_ref_count t_alt_count n_ref_count n_alt_count in Mutect do not match those seen in IGV
I am new to this forum.
I have ran mutect against 2 bam files of the same patient (normal and tumor). the duplicated reads were not marked.
There is a discrepancy between what I see in IGV and different parameters output generated by mutect.
for example: Gene CTNNB1 chr3:41266097 mutation G>T protein D32Y
here are the values from mutect of t_ref_count t_alt_count n_ref_count n_alt_count tumor_f
58 45 414 0 0.436893
When opening the BAM files using IGV, I can see the following:
t_ref_count t_alt_count n_ref_count n_alt_count
200 57 538 0
and obviously the tumor_f which is = t_alt_count/(t_ref_count + t_alt_count) = 57/257=0.2217
Why these values are inconsistent between mutect and IGV ?
Thanks a lot.