This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
combineGVCFs with duplicate sample id?
I am performing the joint calling workflow on a large batch of samples and I have a handful that were sequenced twice, using two different capture kits. For these, the sample ID in the GVCFs are the same. I am looking for an option like -genotypeMergeOption UNIQUIFY to combineGVCFs that will make the sample names unique. I see that if two GVCFs with the same ID are given to combineGVCFs that the ID is present only once in the resulting combined GVCF header, and if the ID is present in two different combined GVCFs that are given to genotypeGVCF that the ID is only present once in the output. What is the recommended practice here? I would like to avoid rerunning my pipeline again to make the names unique in the single sample GVCF.