Hello
I am using Mutect2 in GATK v4.1.4.0 to look for somatic variants in several tumor samples with matched germline. Because of the nature of the samples, I know I can trust variants with relatively low VAF, so I wanted to relax the filtering to allow tumor variants with an LOD similar to that of germline variants (~ 2.2). In previous versions of Mutect2 I would have simply set --tlod at 2.2 during the filtering step. The newest versions of Mutect2, however, does not have this option anymore and relies instead on a beta score (--f-score-beta) to tighten or relax the false discovery rate during the filtering step.
The issue with the beta score is that if I relax the filtering to a point where variants with TLOD >= 2.2 pass the filter, I end up with many variants with very low values in other fields (e.g. STRANDQ=1).
I could relax the filter to allow TLOD >= 2.2 and then filter again manually the resulting VCF to remove variants with low values in other fields, but this seems a rather convoluted way of approaching this issue and it feels like there should be a better way to do it.
In short, is there a way in the latest Mutect2 versions to allow for variants with low TLOD to pass the filtering step without relaxing all filters in the other fields?
Thank you!
I am using Mutect2 in GATK v4.1.4.0 to look for somatic variants in several tumor samples with matched germline. Because of the nature of the samples, I know I can trust variants with relatively low VAF, so I wanted to relax the filtering to allow tumor variants with an LOD similar to that of germline variants (~ 2.2). In previous versions of Mutect2 I would have simply set --tlod at 2.2 during the filtering step. The newest versions of Mutect2, however, does not have this option anymore and relies instead on a beta score (--f-score-beta) to tighten or relax the false discovery rate during the filtering step.
The issue with the beta score is that if I relax the filtering to a point where variants with TLOD >= 2.2 pass the filter, I end up with many variants with very low values in other fields (e.g. STRANDQ=1).
I could relax the filter to allow TLOD >= 2.2 and then filter again manually the resulting VCF to remove variants with low values in other fields, but this seems a rather convoluted way of approaching this issue and it feels like there should be a better way to do it.
In short, is there a way in the latest Mutect2 versions to allow for variants with low TLOD to pass the filtering step without relaxing all filters in the other fields?
Thank you!
