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FilterMutectCalls - Why is the default value of paramer --max-alt-allele-count is 1?
In a tumor sample there are often more cell sub-populations (sub-clones) and there could be a possible contamination of the healthy tissue.
Why have you decided to filter-out the sites with more than 1 alt alleles? Are there biological or technical / informatic reasons? It seems a value too strict which could lead to lose specific sub-clones mutations.