VQSR error: "The provided VCF file is malformed at... "
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?