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?



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