Home

Welcome to the phaseRB wiki!

ReadBackPhasing is a way of phasing haplotype using the called variants (VCF) file along with aligned BAM reads that supports 2 or more adjacent heterozygous variants. This tutorial is a part of Haplotype phasing (GenomeWide or Chromosome Wide), but here we intially only talk about preparing short to medium sized blocks using phaseRB - a python application to phase haplotype blocks using ReadBackPhasing method. This tool forms the first part of the phaseIT pipeline which is on progress.

• The output from this initial RBphasing can be used for downstream genome wide haplotype phasing, but we won't run full genome wide haplotype at this step. Initially we produce short to medium sized haplotype blocks for a given sample.
• When short haplotype blocks are produced for several samples,for example: mom,dad and child (trio based), or several samples from one population or species (population based), this short haplotype blocks are then used together to produce long haplotypes and/or possibly genome wide haplotypes for a sample of interest by looking into LD patterns across other samples.

Requires: Sample BAM, and VCF file in gzipped format along with it's tabix index file.

---

Check out the Tutorials & Happy Phasing !