Phasing

The pipeline supports read-based phasing of variants using DRAGEN (within ~150bp). Variants that are phased together are annotated as belonging to the same phase set, and can be interpreted as variants in cis. Variants will be prioritised as compound heterozygous in biallelic genes if (i) they have phase information and they phase to separate haplotypes or (ii) they do not have phase information.

Not all variants within ~150bp will be phased, therefore alignments need to be inspected in IGV for the variants that are within the distance that could be covered by a read or read pair. Futher guidance on this process can be found in the Variant Review SOP.