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Use VariantsToTable to extract alternate allele count

I'm using the following VariantsToTable command options to extract fields from a VCF file:

/usr/lib/jvm/jre-1.8.0-openjdk/bin/java -Xmx8g -jar /home/1GenomeRef/GATK/GATK_3.5/GenomeAnalysisTK.jar \
-T VariantsToTable \
-R ref.fa \
-V file1.vcf \
--showFiltered \
--out outputfile \

This extracts the correct information, but my original VCF file reports each sample genotype (GT field) as an alternate allele count (0/0, 0/1 or 1/1) and the new output file reports the genotype as the base (C/T, for example.) So the GT for sample1 in my original file might be "0/1" but in the new file it's recoded as "C/T."

I prefer to retain the original genotype format but do not see an option that allows me to request this. Is there an option I can use for this? Or another tool I can apply that will quickly recode the new VCF?

Thanks so much. (And I am following the Best Practices Guidelines - although we are using GATK version 3.5, this is a choice we made for the purpose of ensuring the highest possible consistency with older data called using version 3.5)


Best Answer


  • AEGentryAEGentry Member

    Thank you, @shlee for the very quick and helpful response.

    I decided to use VCFtools to extract the information I wanted using the command:

    --extract-FORMAT-info GT

    It's not optimal because the VCFtools commands are generally less flexible, but it serves the purpose for now.

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