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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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question about --bed #252

Closed brentp closed 3 years ago

brentp commented 3 years ago

Hi Mike, thanks for the great software. If I have a setup so I am calling glnexus with a single chromosome (* $n samples), do I need to specify the --bed argument with the extent of that chromosome for maximum efficiency? or will glnexus split the work correctly on just the chromosome contained in the set of gvcfs? thanks, -Brent

mlin commented 3 years ago

@brentp It shouldn't make a difference for chromosome-split WGS data. For WES or panel data, it's helpful to specify to the target regions (if the GVCF aren't already so filtered) to avoid spending a lot of time on sites that are only covered unintentionally.

brentp commented 3 years ago

great. Thanks!