What are the most important filters provided by Mutect2 and how should we order them based on their priority?
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19 months ago
Researcher ▴ 70

Hi All,

I want to prioritize the functionally relevant somatic variations in cancer normal pairs for which I used Mutect2. Looking at the vcf I found only 10% have passed all the filters and there are many which do not qualify one or more filters defined by Mutect2 as given below:

-alt_allele_in_normal,Description="Evidence seen in the normal sample",
-clustered_events,Description="Clustered events observed in the tumor",
-germline_risk,Description="Evidence indicates this site is germline, not somatic",
-homologous_mapping_event,Description="More than three events were observed in the tumor",
-multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal",
-panel_of_normals,Description="Seen in at least 2 samples in the panel of normals",
-str_contraction,Description="Site filtered due to contraction of short tandem repeat region",
-strand_artifact,Description="Evidence for alt allele comes from one read direction only",
-t_lod_fstar,Description="Tumor does not meet likelihood threshold",
-triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD"


I am not sure among them which are the most important ones and must be considered for calling somatic events and which can be overlooked.

Any suggestions would be highly appreciated. Thanks

mutect2 somatic variations cancer normal pair • 1.3k views
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Entering edit mode

Here my concern is I am left with few thousands of sites (~2000) even in a WGS data from human genome, which looks quite weird. I am looking for any suggestions, Is it really ok to have such a few call from WGS data using mutect2?