Genotyping of fragments with discordant bases

[andurill]

In the current version of GBCM, when a discordant base in encountered between reads in a fragment, and one of the base is "N", its not taken into REF or ALT genotyping. For example, in the screenshot below, the discordant base between the 2 reads in a fragment is highlighted - "T" in one read and "N" in the other. This fragment was excluded from ALT genotype count. While this is the desired behaviour in cases where specificity is important, it will be useful to have an option to prioritize sensitivity. Adding an optional argument that will enable counting these fragments towards genotype counts will be very useful. To elaborate, using this reference case, if the base at the position in one of the reads in the fragment is "N" and the other is "T", it should count towards alt genotyping in the sensitivity mode. Whereas if one is "N", and the other is "G", it should count towards ref genotyping.

If however, neither of the bases is "N", and there is discordance between the reads, that fragment should be excluded from genotyping, even under the sensitivity setting (this is the current behaviour and should be retained).

Test data available on the juno server.