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FastQ to VCF - known indels and SNPs VCF files as vcf.gz

fiapintofiapinto PortugalMember


I have followed the GATK Best Practices to go from fastQ to VCF files with success thanks to the great documentation you have!

I would like to know if the known indels and SNPs VCF files passed to IndelRealigner and BaseRecalibrator really have to be unzipped or if the tools accept the vcf.gz versions?



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