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 Can I merge haplotypes to MNPs in GATK4
I was using GATK 3.8 previously, and I identify MNPs in haploid sequences by first using HaplotypeCaller and GVCFs and then ReadBackedPhasing using the enableMergeToMNP option. But GATK4 seem to have discontinued the ReadBackedPhasing tool, and I am at a loss on how I could have phased SNPs for my haploid (prokaryotic) genome merged to MNPs where the case arises. I will appreciate your help, so I could start using the current version of GATK4.