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Mutect2 Un-filtered variants
Hi GATK Team,
I am working on converting out pipelines from a very old version of Mutect (SATK, somatic analysis tool kit jar based) to the current version of Mutect 2 (GATK 4.0.11).
Previously Mutect2 produced a VCF with both Passing and Filtered variants. I found this post (https://gatkforums.broadinstitute.org/gatk/discussion/7154/mutect2-output-format) that states that variants now show "." for Passing variants in the Filter column, but I am not seeing any filtered/rejected variants in the final output. Is there a way to have Mutect2 output a vcf with filtered variants as well as Passing variants? Also, I do not see any filter lines in the VCF header, I feel that I may be missing a Mutect2 option.
Below is my command (on separate lines for readability):
/apps/gatk4/gatk-126.96.36.199/gatk-188.8.131.52/gatk --java-options "-Xmx4g" Mutect2
I also am seeing in some forum posts about the FilterMutectCalls tools, but I am not seeing any mentions of some of the most commonly filtered reasons that I saw in stats file in the old version of Mutect, for example triallelic_site, fstar_tumor_lod, nearby_gap_events, seen_in_panel_of_normals etc. Is FilterMutectCalls only intended for further filtering, or is this responsible for all Mutect variant filtering?
Two other quick questions. Is the LOD discussed in the tool documentation the Allele Frequency? Is there a tool available in GATK4 to produce a coverage file for positions that reflect what number of reads Mutect used to make variant calls?
Thank you for your help!