MuTect2 strandbias + TLOD clarification
I have a set of tumour samples and I would like to call variants using MuTect2 without matching normals, annotate using VEP and filter out known germline variants afterwards.
I used tumor-only mode with downsampling process turned off. There are a number of artefacts that are being called and I found at least one variant that looks real but was not called. I could think of two options to improve the calling, hence my questions
1- Strand bias: How can I find information about strand bias? I am looking for details like what we typically see in call.stats output of MuTect (ie lod scores of forward and reverse strands), but have not been able to modify my code to include that information. I think some artefacts may be due to strand bias.
2- TLOD : This is where I got confused. Could you explain how MuTect2 calculates TLOD in the absence of matching normal? I use the LOD scores to determine real calls. The majority of real variants would have massive TLOD compared to all calls within each sample. But in my set of samples, there was one variant that seems to be true and had small value of TLOD. I started to think that MuTect2 has to have something as normal to generate correct TLOD, but I am not sure.
This is what I ran:
gatk Mutect2 \
-R hg38 \
-I test.bam \
-L interval_list \
-O test.vcf \
-tumor test.bam \
--contamination-fraction-to-filter 0.0 \
--max-reads-per-alignment-start 0 \
Any comments would be highly appreciated.