Take genotype likelihoods or raw counts as input - Githubissues

dwinter / accuMUlate

code for calling mutatons from MA lines

MIT License

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Take genotype likelihoods or raw counts as input #22

Open dwinter opened 8 years ago

dwinter commented 8 years ago

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 commented 8 years ago

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