[RFE] haplotypecaller: support for custom GVCF GQ slices

[ntm]

Hi,

GATK4 allows to specify custom boundaries for the GQ slices used to group consecutive non-variant positions into a non-variant block, with --gvcf-gq-bands . This feature is quite useful IMO, as the resulting GVCFs can be much smaller (and much faster to work with downstream). The only "loss" is fine-grained resolution of GQ slices for non-variant blocks, but only in the GQ ranges that the user decided he doesn't care about.
It would be great if a similar feature could be implemented in elPrep!

Regards,
Nicolas

[matthdsm]

This seems like something that can be done using GATK ReblockGVCF, which will be part of the updated Broad WGS guidelines

M