PGT/PID fields Mutect2

Hello! I am using Mutect2 as variant caller for whole exome sequencing tumor/normal sample pairs data.
I have seen that sometimes (not often) the mutation sites presented the PGT/PID fields.
For example:
chr21 46086719 . A G . PASS ECNT=2;HCNT=2;MAX_ED=1;MIN_ED=1;NLOD=4.21;TLOD=80.59 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1 0/1:29,26:0.488:8:18:0.692:0|1:46086718_G_C:947,865:8:21 0/0:16,0:0.00:0:0:.:0|1:46086718_G_C:534,0:7:9
chr22 32759025 . G C . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=14.40;TLOD=106.85 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:83,46:0.363:21:25:0.457:2937,1465:47:36 0/0:57,0:0.00:0:0:.:2058,0:28:29
Why in the first example are present the PGT/PID fields and in the second no?

Thank you in advance




  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Those are the phasing annotations which tell you the phased genotype (PGT) and phased ID (PID). Only sites that are phased will have those annotations. Have a look at this post for more information.


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