Dear community members,
I have a small project about calling mosaic variants in ~40 genes in healthy tissue (no obvious neoplasms) in humans. This is not a project that will end up in a paper and thus I do not want to spend a lot of time on it. That's why I have tried to run several mosaic callers and gave up - they sometimes fail for unknown reasons and the results are not that great in terms of accuracy (some of known mosaics are missed).
We have a well-established calling pipeline with FreeBayes. Can I simply lower detected Allele Frequency and turn off the ploidy assumption? I still require sum of base quality to be at least 90 (which means at least 3 good bases in 3 reads to support the variant), but I don't really want to lower it. What are the drawback of Germline Caller usage for Mosaic variants calling?
