Genotype and AD in Mutect2 vcf output

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Ester Feldmesser

• February 02, 2023 13:56

 Why do I see the following genotypes and AD:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	196_A51_H3	WT
chr10	3125031	.	G	A	.	PASS	AC=30;AN=60;AS_FilterStatus=SITE;AS_SB_TABLE=61,33|3,1;DP=1492;ECNT=2;GERMQ=93;MBQ=34,34;MFRL=176,183;MMQ=60,60;MPOS=37;POPAF=7.30;SF=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14;TLOD=7.31	GT:F2R1:SB:DP:F1R2:AD:FAD:AF	0/1:15,2:29,12,3,1:45:20,2:41,4:36,4:0.119	0/1:20,0:32,21,0,0:53:21,0:53,0:43,0:0.022

I understand that sample 196_A51_H3 is a heterozygote, and the AD for the REF allele is 15 and for the ALT allele is 2. I think that the WT sample is homozygote for the REF allele, still the genotype is 0/1 and the AD for the REF allele is 20 and 0 for the ALT allele.

Can you please tell me if I have made an error in my interpretation or why the WT genotype is written as 0/1?

GATK version was GATK 4.3.

Thanks

 

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  David Benjamin

  • February 06, 2023 18:17

  Ester Feldmesserin The GT field in Mutect2 is basically meaningless -- 0/1 in the tumor and 0/0 in the normal is merely an indicator of a somatic variant, but the concept of an integer genotype isn't really well-defined when it comes to somatic calling.

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