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VariantsToTable for multi-sample VCF's?

summerelasummerela Seattle, WaMember
edited March 2015 in Ask the GATK team


Will VariantsToTable work for multi-sample VCF files? I've tried the following command, but it only outputs the column headers:

java -jar ~/tools/GenomeAnalysisTK.jar -R chr1.fa -T VariantsToTable -V cg_100.vcf.gz -F CHROM -F POS -F ID -F REF -F ALT -F F-101-009 -o test.table


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It should work; try dropping that last field, which looks unfamiliar to me.

  • summerelasummerela Seattle, WaMember

    Hi Geraldine-

    Thanks so much for the quick reply. I did try with and without that last field (it's a sample name I tried adding to see if that made any difference) and it does not output anything. I tried ommiting all but the CHROM, POS, ID, REF and ALT fields, as well. I followed your guide for building the reference dict and fai files, indexed the VCF with tabix.

    The VCF files are CGI, not illumina, does that make any difference?


  • summerelasummerela Seattle, WaMember

    Thank you, I'll test it out and let you know!

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