Platypus variant calling outputs VCFv4.0 with no contig ID
Dear all,
I am running platypus to do variant calling. As regions I am suing chromosomes short and long arm separately, in order to make the process fast. When I try to merge the output vcf files as the end, I get an error that the contig is not present in the vcf file. Thats because Platypus outputs VCFv.4.0 which does not have contig ID, compared to VCFv4.2 which does. Is there any solutions to overcome this?
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