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what is max-alternate-alleles ?
firstly ,set max-alternate-alleles is 6 .
I guess max-alternate-alleles means that at a site , the ref allele is A , the number of other alleles type (C,G) found by reads do not more than 6 . but as we know , just total 4 base types : A,T,C ,G , so I think the max-alternate allele will count indel at a region ,not a point putation.
the max-alternate-alleles setting only is available for indel region ,rather than point mutaion site .
Am I right ?