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How Can I merge haplotypes to MNPs in GATK4

mezewudomezewudo AtlantaMember

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.


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