Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GT values of VCF file generate by Mutect2



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    Fiona Liang

    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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    Gökalp Çelik

    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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