Output reference allele length `REF` in result VCF

[dnil]

E.g. ExpansionHunter would output the reference allele length as determined for the current locus definition, reference genome sequence and caller version. This feels like a rather good practice, especially given the output of ALT as . for GT 0/0 hom ref calls. It looks like it is computed internally in TRGT anyway?

##INFO=<ID=REF,Number=1,Type=Integer,Description="Reference copy number">

[tmokveld]

Hi Daniel,
Thanks, it’s a great idea. Is this the same feature requested in this issue?
In any case I will dig into this and decide where best to slot it into our roadmap.

[dnil]

Slightly different, but with considerable overlap! I would leave it to you to decide what is possible and useable: perhaps having only a single ref-size is no longer a good trade off, and something MC-resolved would be more appropriate. The main use-case for us would be a numerical repeat size guesstimate even when the alt allele call is ".", so a "0/0" genotype.