Skip to content

Latest commit

 

History

History
17 lines (13 loc) · 1.2 KB

README.md

File metadata and controls

17 lines (13 loc) · 1.2 KB
Raw

Haplotypo

Docker Pulls run with docker

This repository contains the Haplotypo pipeline.

Description

HaploTypo is a pipeline suited to map variants into haplotypes in genetic variation analyses. After mapping and variant calling on a phased reference genome, HaploTypo infers the haplotype correspondence for each heterozygous variant. It also generates two independent FASTA files for each reconstructed haplotype.

Scripts contained in this repository:

  1. mapping.py -> pipeline for read mapping with BWA-MEM
  2. var_calling.py -> pipeline for SNP calling using one of the programs: GATK, bcftools or freebayes
  3. VCFcorr_alleles.py -> script for to find the correspondence of SNPs between the two haplotypes and output a corrected VCF (only SNPs that actually belong to this haplotype)
  4. haplomaker.py -> script to reconstruct the two haplotypes taking the corrected VCF
  5. haplotypo.py -> pipeline to automatically run all the other pipelines
  6. programs_config.py -> file to set the path of each program