What should I do with vcf file now
Answered
Hello
I have called SNVs with Mutect2, now I filter column of a file called filtered vcf I have a lot of things like
> length(unique(filtered.vcf$FILTER)) [1] 409 >
> unique(filtered.vcf$FILTER) [1] "germline" [2] "PASS" [3] "clustered_events" [4] "clustered_events;panel_of_normals" [5] "weak_evidence" [6] "haplotype" [7] "base_qual;haplotype" [8] "clustered_events;germline;haplotype" [9] "base_qual;clustered_events;germline;haplotype" [10] "clustered_events;haplotype" [11] "clustered_events;haplotype;weak_evidence" [12] "base_qual;clustered_events;haplotype" [13] "haplotype;map_qual"
I don't know I should keep PASS ones or what else
I supposed the filtered.vcf output contains only the filtered events
Help me please
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Hi mina ming,
All variants are listed in the VCF file but only variants marked with PASS have passed filtering. You can read more about the filter column in this article: https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format
If you want the filtered VCF with only your filtered variants, you can fun Funcotator with --remove-filtered-variants true or SelectVariants with --exclude-filtered true.
Please let me know if you have further questions.
Best,
Genevieve
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