The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Specify vcf fileformat
After running gatk, I further process the VCF file using pyvcf, which only supports VCFv4.1. With gatk3.6, it gets confused by the ##FORMAT, Number=R setting, which is new in VCFv4.2.
Is there a way to 'downgrade' a VCF file to an earlier format, or to instruct the GATK to output a certain version of the VCF file format?