MuTect2 tumorOnly vs paired loses true variants
Hi GATK team !
I have an issue with MuTect2. I'm using GATK last version (nighlty build from 16th of March) in a somatic context on an amplicon design.
I have a variant that I know is true one (although the depth of coverage at this position is quite low in the somatic context).
MuTect does call the variant when in tumor only mode : first one if the 3 here
chr13 32900222 . C T . clustered_events;homologous_mapping_event ECNT=3;HCNT=45;MAX_ED=45;MIN_ED=41;NLOD=0.00;TLOD=39.33 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:85,36:0.149:36:0:.:2087,972:83:0
chr13 32900263 . G A . clustered_events;homologous_mapping_event ECNT=3;HCNT=16;MAX_ED=45;MIN_ED=41;NLOD=0.00;TLOD=8.56 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:1020,18:8.696e-03:18:0:1.00:26997,444:1020:0
chr13 32900267 . C T . clustered_events;homologous_mapping_event ECNT=3;HCNT=5;MAX_ED=45;MIN_ED=41;NLOD=0.00;TLOD=6.81 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:1024,16:0.015:16:0:0.00:27735,411:1024:0
It seems like it considers the 3 variants to be clustered and on the same haplotype, that may be important for my issue ? Although 222 from 263 is already quite far away..
When calling in paired mode, feeding it with the recalibrated germline bam file, I have no variants left, even though neither of these 3 variants is a germline one.
Could you please tell my the reason why those variants are filtered out ? Is there a parameter I should play with ?
thanks a lot