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

fiapintofiapinto PortugalMember

Hi,

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?

Thanks,
Sofia

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