Mutect2 missing mutations

Question

[vctrm67]

I am using the latest version of Mutect2 (4.1.9.0) and trying to call mutations from Mutect. I noticed that Mutect is not calling muations with clear read support in IGV. I tried some suggestions found on this forum like this but they didn't help. You can see the mutation here:

This is a call for a BAM file that doesn't have an associated normal file. I run Mutect2 and this is the command through Cromwell:

${gatk_path} \
    Mutect2 \
    -R ${ref_fasta} \
    -I ${input_bam} \
    --panel-of-normals ${panel} \
    --germline-resource ${gnomad} \
    --f1r2-tar-gz f1r2.tar.gz \
    -L ${regions_list} \
    -O ${output_filename}

The regions list that I use is simply a file that splits the reference into different regions to call. I do not specify particular regions to call, simply to break up the calling into chunks.

There should be a mutation somewhere between chr13:32,914,430-32,914,440 in the photo, I think it is at 32,914,440 based on the photo. Is there anything else I can try?

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)

[igor]

Have you checked the VCF? It should contains all variants with reasonable evidence. Most will not be classified as passing. If not passing, they will have specific flags listed that caused them to fail.