My genomes are all males but the merged deepvariant calls for Y are diploid instead of haploid (and I do not know where the PAR region are in rat if present).
I would like to extend the 'DeepVariantWGS' config with a yaml file containing something like
# config.yaml
ploidy:
chrY: 1
chrX: 1
but the command takes only a single -config argument
Is there a way out to my problem or is the damage done in deepvariant prior to running GLnexus for merging?
Hi,
I have a related issue to #291
My genomes are all males but the merged deepvariant calls for Y are diploid instead of haploid (and I do not know where the PAR region are in rat if present).
I would like to extend the 'DeepVariantWGS' config with a yaml file containing something like
but the command takes only a single -config argument
Is there a way out to my problem or is the damage done in deepvariant prior to running GLnexus for merging?
thanks in advance
deepvariant:1.5.0 GLnexus:1.4.3