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mutect2 output filter field

Hi!
I ran mutect2 and I got the vcf file, but I didn't understand the output. For example I have this line in my vcf:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample13

chr1 10715958 . T TCTTGGCATATG . alt_allele_in_normal ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=17.05;TLOD=7.63 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:100,3:0.030:1:2:.:3647,109:53:47
chr1 11585340 . CCTGGGG C . alt_allele_in_normal;clustered_events ECNT=4;HCNT=34;MAX_ED=19;MIN_ED=6;NLOD=61.78;TLOD=11.61 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1 0/0:327,5:0.018:3:2:.:0|1:11585334_GTGTC_G:11686,189:153:174
chr1 16956555 . C T . alt_allele_in_normal;t_lod_fstar ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=6.46;TLOD=4.81 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:64,2:0.040:2:0:0.00:2105,75:28:36

why I have, for example, both alt_allele_in normal and clustered_events or t_lod_fstar, or only alt_allele_in_normal? what does it mean?
Thank you in advance,
best

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  • johnmajohnma Member

    Have you actually read the MuTect paper to begin with? These are independent hard filters for MuTect outputs and a position can fail for one or more of these filters.

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