Closed pdiakumis closed 2 years ago
The CSQ metadata line in the somatic VCF can get out of sync with the VEP options specified in PCGR, which can be confusing for downstream users. See https://github.com/umccr/vcf_stuff/blob/110f115d7c541c06209e0acf4ff3dbc36874e651/vcf_stuff/filtering/annotate_somatic_vcf.smk#L402 and the attached diff. We should probably read that directly from the PCGR output file instead of hard-coding it.
The CSQ metadata line in the somatic VCF can get out of sync with the VEP options specified in PCGR, which can be confusing for downstream users. See https://github.com/umccr/vcf_stuff/blob/110f115d7c541c06209e0acf4ff3dbc36874e651/vcf_stuff/filtering/annotate_somatic_vcf.smk#L402 and the attached diff. We should probably read that directly from the PCGR output file instead of hard-coding it.