Error when running VariantRecalibrator
I'm running the VariantRecalibrator with input HC gVCF file that was created by GenotypeGVCFs on a list of 66 samples. I'm getting an error message: "MESSAGE: Line 474547: there aren't enough columns for line".
All input vcf lines contain the same #columns. I tried the same command several times and got same error message with different line number.
also, the same command that I used with another input file (with less samples, 57), is running fine.
Please advise - are there parameters I should change to handle a larger input file?