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VariantsToTable only returning header lines

wigge206wigge206 Member
edited July 2018 in Ask the GATK team

Hi when running VariantsToTable the output.table produces only the header. I can't see anything that would cause this to happen.
I am using gatk-4.0.6 with the following settings.

./gatk VariantsToTable -V test.vcf -F CHROM -F POS -O output.table

The vcf header is too long to paste but can provide that if needed.

All I'm getting back is

CHROM POS

If I include -GF GT I get back all the sample IDs but again only header information.

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