This repository contains the Haplotypo pipeline.
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:
- mapping.py -> pipeline for read mapping with BWA-MEM
- var_calling.py -> pipeline for SNP calling using one of the programs: GATK, bcftools or freebayes
- 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)
- haplomaker.py -> script to reconstruct the two haplotypes taking the corrected VCF
- haplotypo.py -> pipeline to automatically run all the other pipelines
- programs_config.py -> file to set the path of each program