GatherVcfs to concatenate GVCFs
GATK version used: gatk4-4.2.6.1-0/gatk-package-4.2.6.1
Dear GATK experts,
I am trying to concatenate multiple GVCFs (all same samples, different genomic intervals) but having the following error:
A USER ERROR has occurred: Couldn't read file file:///mnt/shared/scratch/ssharma/private/tsb_spet/intervalwiseCombinedGvcfs.spet.tsb/spet.tsb.SPET.final.variants.g.vcf.gz
I have checked all input files are fine and in the correct genomic order.
If possible a prompt reply would be helpful even just to clarify whether GatherVcfs can also be used to combine GVCFs or this tool is only for VCFs.
Regards,
Sanjeev
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Hi sanjeevksh,
Thank you for writing to the GATK forum! I hope that we can help you sort this out.
Unfortunately, GatherVcfs (Picard) cannot concatenate GVCFs. The good news is that we have another GATK tool called CombineGVCFs that will do the job.
Please give this tool a try and let me know if you find success. If any other questions arise in the meantime, please do not hesitate to reach out.
Best,
Anthony -
Hi sanjeevksh,
We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!
Kind regards,
Anthony
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Hi Anthony (Anthony DiCi)
Thank you for your feedback. I have used CombineGVCFs several times before for combining GVCFs from multiple samples but didn't realise it can be used for concatenating GVCFs as well. On this occasion, I have used GenotypeGVCFs on the per-interval generated GVCFs and converted the output vcfs into a single vcf using GatherVcfs but your feedback will be helpful going forward.
Regards,
Sanjeev
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