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@davidben I might have some more insight from the tumor-only mutect runs: Like I said, running Mutect2 in tumor-only mode equalizes the number of variants a bit. Then I used FilterMutectCalls, filtering out positions in both samples and then filt…
@davidben thanks for your response! I seem to have made a mistake and looked at the wrong files: The before numbers should have been about 30500 and 4000. The 6400 and 700 were after my own filtering on depth which I accidently turned on. Sin…
To see if it depends on the normal I ran Mutect2 in tumor-only mode for these samples. The results are about 26000 and 46000 variants each before FilterMutectCalls and 20500 and 22600 variants after FilterMutectCalls. In this case, it seems that Fil…
Interestingly, the depth in the normal sample is lower in positions of the low-variant sample. See https://imgur.com/a/oRcws9g for a normalized histogram. So looks like Mutect2 calls more variants if the depth in the normal is higher. This still doe…
Before FilterMutectCalls it's equally large of a difference (6400 vs 470). I think I am not allowed to share my vcf's, as the data is not public (from EGA). I'll try to make the histogram for normal calls today or monday and come back asap, than…
@davidben Yes this is with the same normal sample.
Thanks for the response @bshifaw The thread that you linked has some very useful responses, I mainly was not aware that for Exome Sequencing it is recommended to use the -L command with exon regions for speed, I will try this. But the responses …