How to set threshold to filter vcf files about deepvariant

[lucasbrambrink]

Hi, thanks for the question.

1. RefCalls are candidates that were determined to match the reference and are therefore not variants. They are still included in the VCF file to show they were considered, since it can be just as important to know with high confidence that a particular variant does not exist as it is to know that it does exist.

2. The postprocess_variants step applies quality filters, which can be set via flags.

   • --qual_filter will remove any variant with QUAL < qual_filter.
   • --cnn_homref_call_min_gq will set RefCalls to ./. instead of 0/0 with GQ < cnn_homref_call_min_gq
   • --multi_allelic_qual_filter will remove multi-allelic variants with QUAL < multi_allelic_qual_filter.

The default value for --qual_filter is 1.0. If this is too low, you can set this to a higher value using the --postprocess_variants_extra_arg flag in run_deepvariant, e.g. --postprocess_variants_extra_args="qual_filter=5.0"

I hope that helps!

[Tonitsk8264]

Thank you for your prompt reply !