Thought I'd throw this one out into the void in case anyone has any ideas... Say I have a reference and some Illumina reads. Is there an easy way to phase the reads by haplotype so I have a fastq of reads from one haplotype and another of reads from the other? The goal is to generate some fake trio data for a test dataset - I have reads from the "child" which I can phase by mapping directly to the hap1/hap2 reference I have, but need to get some haplotype-specific reads to blend in from the "mother" and "father".

Maybe ask in the #C05G7UE94CT channel? Even if it is not the main functionality of the pipeline, I presume that crowd is most knowledgeable with regard to your problem as well?

Thanks for the suggestion, I've thrown my question over there too!

it's going to be complicated. I guess you would call variants and then phase and then go backwards to the fastqs https://whatshap.readthedocs.io/en/latest/guide.html#creating-phased-references-in-fasta-format