I'm needing to utilize chrM variant calls from the bulk whole genome variant call files (gVCFs, field 23191) to feed into GLNexus for joint genotyping. The participant EIDs for my project match in the filenames of the gVCFs but not the sample IDs in the body of the gVCFs. I can use BCFtools to rename the sample name in the gVCF body to match that of the EID in the filename but I was wondering if there is a recommended way to handle this?
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Hi @Katreya Lovrenert?, is this helping you to resolve this? https://dnanexus.gitbook.io/uk-biobank-rap/frequently-asked-questions#are-the-headers-of-gvcf-or-cram-files-pseudonymized
Thanks. I came across this very FAQ after posting the question. Everything is good now.
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