GT values of VCF file generate by Mutect2
Hi All,
I ran the "Somatic short variant discovery" pipeline on my WES data and I found only 2 kinds of values in GT(0/1 and ./.).
I wonder whether all my SNVs are heterozygous sites.
Thank you in advance!
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Some answers are explained like this:
GATK assigns the genotype "0/1" for single nucleotide variants (SNVs) instead of "1/1".
Is it true?
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Hi Fiona Liang
Genotypes assigned by Mutect2 does not really reflect the actual genotype in fact the main output is the detected allele fraction and other balancing and supporting factors for the trueness of the call.
For HaplotypeCaller the genotype is dependent on allele count, supporting read counts and ploidy.
We also a few questions here to clarify your case.
Is your data a deep sequenced tumor data? Are you using GVCF mode?
Can you provide more specifics like your command line, kind of data you are working on?
We may be able to help better with these information.
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