calling haploid chromosomes

[splaisan]

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

# 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?

thanks in advance

deepvariant:1.5.0
GLnexus:1.4.3