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

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @edAL
    Hi,

    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.

    -Sheila

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