I have a WGS dataset in which indels were also called. Now I am looking towards creating this a reference dataset for the local population I am working on. But before using this as a reference set for imputation of Exome data for samples from this population, I would need to phase this WGS dataset.
The problem is that SHAPEIT and MACh can't handle indels within the files and usually have to be removed before phasing. My query is how do I phase the WGS dataset but also preserving the indels within it.
Any help is greatly appreciated!