New v2 pipeline

[gevro]

Hi, In the new v2 pipeline, there is no option to turn off tertiary analysis. Does the pipeline still output the primary VCF calls before tertiary analysis is performed? Since we want the raw vcf files, as we use our own custom annotations and filter thresholds. We don't want only tertiary vcf files.

Thanks

[williamrowell]

In the new v2 pipeline, there is no option to turn off tertiary analysis.

From the input documentation for the family.wdl workflow:

File?   tertiary_map_file   If omitted, tertiary analysis will be skipped.

Does the pipeline still output the primary VCF calls before tertiary analysis is performed?

Yes, the unfiltered VCFs are output regardless of whether tertiary analysis runs.