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Mutect2 vcf output including 0|1 instead of 0/1

SPPearceSPPearce Manchester, UKMember
Hi,

I'm running gatk Mutect2 from GATK v4.1.2.0 with a tumour normal pair, and it is completing successfully.
However, some of the rows on the output vcf contain data cells that look like:
"0|1:18,3:0.158:21:15,0:3,2:0|1:34872446_CTGGGTG_C:34872446:17,1,1,2"
instead of most of the cells which look like "0/1:82,7:0.086:89:51,5:30,2:60,22,5,2".

Is this an expected output? If so, what do these mean?
I found it very difficult to search for the special character, so apologies if this is answered somewhere else.

Thanks,
Simon

Example two rows:

19 34872454 . A G . haplotype CONTQ=48;DP=878;ECNT=2;GERMQ=93;MBQ=20,21;MFRL=227,148;MMQ=60,60;MPOS=-1073741824;NALOD=2.69;NLOD=252.15;POPAF=6.00;SEQQ=14;STRANDQ=51;TLOD=4.87 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,3:0.252:13:6,0:1,2:0|1:34872446_CTGGGTG_C:34872446:10,0,1,2 0|0:856,3:1.924e-03:859:510,2:288,1:0|1:34872446_CTGGGTG_C:34872446:469,387,0,3
19 36616725 . C T . PASS CONTQ=48;DP=1152;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=196,175;MMQ=60,60;MPOS=38;NALOD=3.02;NLOD=310.19;POPAF=6.00;SEQQ=33;STRANDQ=54;TLOD=7.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:82,7:0.086:89:51,5:30,2:60,22,5,2 0/0:1036,1:9.588e-04:1037:533,0:502,0:547,489,1,0

Answers

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