Take genotype likelihoods or raw counts as input

[dwinter]

This might be a "next release" sort of goal, as it's beyond what we plan for the paper but would nevetheless be helpful.

At the moment we are only calling SNV mutations because that's what our DM models is good goor.
However, if would be useful to call putative indels, CNVs and other mutations in MA framework. The easiest way to do that would to either

• take counts (i.e. number of reads) for each allele as use the DM model for likelihoods
• take genotype likelihoods calculated from Some Other Software (vcf?) as input and

The latter would require a vcf parser (probably htslib?)

[dwinter]

(we have started work on this, but this will be a long-term goal rather than something to include in the first release)