Great to know that the newer versions of HaplotypeCaller supports custom ploidy regions with the parameter --ploidy-regions:
https://newreleases.io/project/github/broadinstitute/gatk/release/4.5.0.0 : "The main use case is for calling haploid variants outside the PAR for XY individuals as required by the VCF spec".
Is there any guideline to create this customized BED file?
DeepVariant provides similar function with parameter --par_regions_bed and they also provide the BED files to download here https://github.com/google/deepvariant/blob/r1.8/docs/deepvariant-haploid-support.md
Can I just use their PAR BED and invert it to get the non-PAR (haploid) regions, and prepare the BED file to provide to --ploidy-regions?
Great to know that the newer versions of HaplotypeCaller supports custom ploidy regions with the parameter
--ploidy-regions:https://newreleases.io/project/github/broadinstitute/gatk/release/4.5.0.0 : "The main use case is for calling haploid variants outside the PAR for XY individuals as required by the VCF spec".
Is there any guideline to create this customized BED file?
DeepVariant provides similar function with parameter
--par_regions_bedand they also provide the BED files to download here https://github.com/google/deepvariant/blob/r1.8/docs/deepvariant-haploid-support.mdCan I just use their PAR BED and invert it to get the non-PAR (haploid) regions, and prepare the BED file to provide to
--ploidy-regions?