Re-check labelling of mutations as covered, genotyped and not covered.

[rhshah]

@peteryzheng I have seen a couple of times inconsistent labeling from filter_reads.R, can you please check to make sure the same criteria is used overall.

[rhshah]

Just as an example we have sometimes called mutations with 1 ALT ALLELE count as genotyped and sometimes not called.

[rhshah]

@peteryzheng it will be also good to get clarity on when you use Genotype vs Not Called.