Add options: --source-tag option to filter analysis entries to query (e.g. --source-tag nagim for separate the KCCG TOB-WGS from NAGIM).
Remove ExcessHet filter as it is covered by InbreedingCoeff filter. Drop related samples from InbreedingCoeff calculations (however keep them in the dataset).
Add --add-validation-samples/--no-add-validation-samples to control whether to add GiaB trio and syndip into the mix (they are called with BWA/GATK3.5 and can't be combined with Nagim).
Add --release-related flag that controls whether to keep relateds in the release. GnomAD flags relateds and drops from the release, however we want to keep them if we want an acute-care subset.
Add chrX_r_het_hom_var metric for extra sex validation (suggested by DanielM).
--source-tagoption to filter analysis entries to query (e.g.--source-tag nagimfor separate the KCCG TOB-WGS from NAGIM).--add-validation-samples/--no-add-validation-samplesto control whether to add GiaB trio and syndip into the mix (they are called with BWA/GATK3.5 and can't be combined with Nagim).--release-relatedflag that controls whether to keep relateds in the release. GnomAD flags relateds and drops from the release, however we want to keep them if we want an acute-care subset.chrX_r_het_hom_varmetric for extra sex validation (suggested by DanielM).mt.