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Mutect2 with contamination estimates
How many sites does ContEst need to get an accurate answer?
A couple of my samples give me results like this:
name population population_fit contamination confidence_interval_95_width confidence_interval_95_low confidence_interval_95_high sites
META CEU n/a 57.3 0.8 56.9 57.7 83
57% contamination seems very high. Other samples report using around 1000 sites and the contamination comes out around 20%. I wonder if the high result is inaccurate as ConTest is only using 83 sites?
How does mutect2 use the output from ContEst?. I would to like to run Mutect2 with and without the ConTest results, as I am concerned I will get very few SNPs passing if such a high level of contamination is assumed . However Mutect2 is running very slowly and I don't have the compute resources to run it twice. Is there any way I can filter the output of muctect2 to take into account the contamination estimates?
Any thoughts much appreciated