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
1 answer
I would say that this is common - yes. Variants can fail QC in different ways.
You should really ask your collaborator how the value in the FILTER column has been set, though. It could be that they are not even utilising it, in which case it will be set by whatever program has called the variants and using it's default settings (but even the program may not even do this). However, if the collaborator is utilising it, then it may represent just one very fundamental aspect of QC.
Either way, you should check.
Kevin
Log in to answer this question.
-
Handling FILTER Fields in VCF Metadata and Body
written by ManuelDB
-
Please advise a tutorial/course on genetic data analysis
written by Qbit- •
-
How to do sample based QC via bcftools
written by nobody •
-
How to confirm if VCF file is normalized and Left aligned ?
written by nobody •
-
Use bcftools to filter a VCF with multiple filter flags
written by Ram
-
Inconsistent bim files after plink plain text format converting
written by yiqiangz •
-
What are the most important filters provided by Mutect2 and how should we order them based on their…
written by Researcher
-
How to get VCF file into a data matrix form for machine-learning? (new to vcf files)
written by jespinoz •
-
Ideal samtools view f/F flags
written by by0
-
Select Certain Column From Vcf File
written by michealsmith
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.