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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:

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