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!
GenomicsDBImport intervals and haplotaypecaller estimated time GATK 126.96.36.199
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