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datasharing

The Leek group guide to data sharing

hla_genotyping

Tutorial for genotyping, haplotyping, and allele calls for HLA genes

kir_genotyping

Tutorial for genotyping, haplotyping, copy number estimation, and allele calls for KIR genes

mhc-ancestry

phase-readbackedphasing

This script uses the phased data from a GATK ReadBackedPhasing VCF file (to get haplotypes from NGS data) to create a fragmented .known file. This known file will be used with the PHASE algorithm. Then, it compares the PHASE results from multiple runs considering this fragmented .known file.

phasex

Phasex is a software written in C++ to automate and compare multiple haplotyping runs using Shapeit4 and/or Beagle 4.

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