Add an explicit FORMAT/TAG for illumina genotype?

[rajwanir]

Hi @freeseek

Following up on #68, I was wondering if it may be feasible for you to include an Illumina_genotype tag in the FORMAT field? I see that based on ALLELE_A/ALLELE_B and GT the illumina_genotype can be infered. I will look up how I may be able to include this as a post-processing and then pass it on to the downstream tools that need it. But wanted to check if this is something might be straightforward to include in the standard output from gtc2vcf?

The illumina AB genotype could be either in the AA,AB,BB or NN format or it's numerical encoding as described here (https://github.com/broadinstitute/picard/blob/40bc2fd45ec3c0f438f2a4d31139c73dff792c82/src/main/java/picard/arrays/illumina/IlluminaGenotype.java#L35)

Thank you