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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


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