I'm running a cross-contamination test by following the gatk pipeline. I have no problem launching GetPileupSummaries and CalculateContamination as I get results, but I don't understand why the default values keep a max-allele frequency of 0.2 and a min-allele frequency of 0.01 when GetPileupSummaries is launched
(I have read all the information available in GATK and the only thing I have been able to get is: If the homozygous alternate site has a rare allele, we are more likely to observe the presence of REF or other more common alleles if there is cross-sample contamination)
I have done some tests and I get similar results if I use a max-ref of 0.2 or a max-ref of 0.8, so I don't understand why this can be possible
Thanks so much for reading.