I'm working with some VCF files from a collaborator. In the FILTER column of any given VCF I'm used to seeing either PASS or some form of flag; however, in the files I'm looking at now, a reasonable proportion of variants are annotated PASS BUT also have one or more flags e.g. 'alt_allele_in_normal,clustered_events,t_lod_fstar,PASS,homologous_mapping_event,triallelic_site'
Is that normal, or does this suggest something went awry with the raw data processing (I'm awaiting details on the methodology used)? I've never seen this before. Thanks
Thanks- I can see how a given variant could fail for multiple reasons, but the part that doesn't make sense to me is the fact that these variants are ALSO annotated with 'PASS'
i.e. in the above, example 'alt_allele_in_normal,clustered_events,t_lod_fstar,PASS,homologous_mapping_event,triallelic_site'
If it fails QC, why is it also marked PASS?
Thanks
Please ask your collaborator how they processed the data. Like I said, the FILTER field in the VCF may not even be used by them (the collaborators), in which case the software calling the variants will decide what passes or fails based on its own default settings.