varfish-org
tsv output can contain empty sample/genotype-data which causes bugs in varfish
Is your feature request related to a problem? Please describe. In a case/pedigree with multiple samples some variants may not have usable data from all samples (either due to missing coverage or also on the Y chromosome). In vcf files this can either be encoded as a single "." for that sample in the sample/genotype block or with individual missing values for each defined Format field. The tsv output file for Varfish converts fully empty fileds (".") into empty sample specific data (genotype column, i.e. """sample_2""": {} ), which causes bugs in Variant filtration.
Describe the solution you'd like The tsv files generated for varfish should not lead to downstream errors. Ideally all defined format fields of each variant should be written into the genotype data for each sample, with a default value of ".".
Describe alternatives you've considered This could also be fixed on the varfish side.
Additional context Varfish-issue for the bug caused by empty sample data
