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GenomicsDBImport intervals and haplotaypecaller estimated time GATK 18.104.22.168
I'm trying to get VCF file following germline short variant discovery best practices.
I have ready for variant discovery bam files. I have 2 questions:
I need to specify time limit for jobs i submit and also i'm short of time. I want to know how long does haplotypecaller usually takes to get output so i can give the job a good time limit.
what are effective factors?
my bam files are about 10GB each.
GenomicsDBImport needs to get an interval list but i don't have interval list or exclude list and i'm doing whole genome analysis. what should i put for intervals since it's a required parameter and also estimated time to get output for this step if possible.
Thank you very much