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How to pass physical phasing information from HaplotypeCaller 3.4 through to Beagle 4.0?
I have been using HaplotypeCaller 3.4 on five hundred cattle genomes. I am wondering how to pass the physical phasing information, now generated by Haplotype Caller in N+1 mode, through GenotypeGVCF applying pedigree and then out to Beagle 4.0 as a vcf.gz for imputation.
My goal is to make a phased reference that is as accurate as possible to be used as an imputation resource. hence I would like to exploit physical phasing information.
Do you have an example work flow? It seems that the recommendations for read-backed phasing have changed since haplotype caller 3.3 came up with the N+1 workflow.