We've moved!
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!

Error with GenomicsDBImport input file


I am trying to run GenomicsDBImport to test my pipeline with just 2 samples. I am using the following code:

gatk GenomicsDBImport \
-V $SCRATCH/active/memtest2/ SRR112728.raw.snps.indels.g.vcf \
-V $SCRATCH/active/secondex/SRR112730.raw.snps.indels.g.vcf \
--genomicsdb-workspace-path $SCRATCH/active/secondex \
-L 20

I get the error:

A USER ERROR has occurred: Invalid argument 'SRR112728.raw.snps.indels.g.vcf'.

I'm not sure what the problem is with this input file. This is in the format specified in haplotype caller documentation. Can you please advise?


Best Answer


Sign In or Register to comment.