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## Description

HaploTypo is a pipeline designed to perform variant calling and to assign alleles to a given haplotype in the presence of a phased reference genome of a closely-related organism. With HaploTypo you can obtain genome heterozygosity and variant phasing information, with no need to pass through the demanding traditional de novo genome phasing process.

The pipeline is divided into four independent modules, each of them consisting of a separate python script. The modules perform the following steps:

(1) Independent read mapping to each of the haplotypes using BWA-MEM (Li, 2013) (2) Independent variant calling using GATK (McKenna et al. 2010), bcftools (Li et al. 2011) or freebayes (Garrison and Marth, 2012) (3) Inference of the alternative variants for each haplotype (4) Reconstruction of the final alternative haplotypes

First, HaploTypo performs read mapping and variant calling of a given sample independently on each phased reference haplotype (modules 1 and 2). Then, HaploTypo module 3 compares the phased reference haplotypes with the VCF files obtained and phases based on the called alleles and genotype. Table 1 lists all possible cases that may be encountered by HaploTypo when comparing variants called in each of the two haplotypes, and indicates how they are handled and encoded in the output files from module 3. Finally, HaploTypo module 4 takes the information provided by module 3 and generates the reconstructed haplotypes in FASTA format.