Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.