VQSR error: "The provided VCF file is malformed at... "
Posted in Ask the GATK team | Last updated on

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I am seeing this error on single human WGS sample -

The provided VCF file is malformed at approximately line number "x": there are 557 genotypes while the header requires that 1525 genotypes be present for all records

Interestingly, when I run VQSR as part of the same pipeline on the same sample consecutive times, the "x" changes to different line numbers each time. I was wondering if someone could explain the meaning of the error message more?

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