HapFIRE

HapFIRE is a python-based pipeline to calculate allele and genotype frequencies from pool-seq data given founder SNP VCF file.

Please cite the following papers for HapFIRE

• Wu, Xing, et al. "Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana." bioRxiv (2025): 2025-05.

• Kessner, Darren, Thomas L. Turner, and John Novembre. "Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data." Molecular biology and evolution 30.5 (2013): 1145-1158.

Installation

HapFIRE relies on HARP to estimate the haplotype likelihood. To make everyone's life easier, we have included a pre-compiled version of harp (harp_linux_140925_103521). If you prefer to install another version, please replace the executable in the src folder.

Install via mamba

mamba env create -f environment.yml
conda activate hapfire

Required input

• Phased SNP vcf file as the reference panel
• sorted and index pool seq alignment bam file
• reference genome fasta file

Options

-v the phased vcf file 
-b the sorted alignment bam file 
-f reference fasta file 
-s (calculate haplotype frequencies) (True/False ,default: False. ) This step will be very slow and computationally expensive if you perform genome-wide fine block partition 
-p genome-wide block fine block partition algorithm (bigld) 
-c the LD r2 cutoff for more defined blocks (default: 0.5) 
-w window size for calculating independent blocks (default: 100) 
-r the LD r2 cutoff for independent blocks (default: 0.1) 
-o prefix of output files 

Usage

The most common usage of hapfire is to estimate allele and genotype frequency from pool sequencing data

python3 hapFIRE.py -v example/example.recode.vcf -b example/example.bam -f example/example.fa -o test

If you want to estimate haplotype frequency, HapFIRE will first perform genome-wide block partition and then cluster unique haplotypes from each block, and then estimate haplotype cluster frequencies

python3 hapFIRE.py -v example/example.recode.vcf -b example/example.bam -f example/example.fa -s True -p bigld -o test

Program output

• .snp_frequency.txt: The estimated frequencies of alternative alleles in the reference panel from the pool seq data.
• .ecotype_frequency.txt: The estimated frequencies of all genotypes in the reference panel from the pool seq data.
• .independent_genomewide_partition.txt: independent haplotype blocks (LD r2 0.1) identified by hapFIRE
• .fine_genomewide_partition.txt: more defined haplotype blocks identified by user specification (usually bigLD)
• .unique_haplotype_frequency.txt: The estimated frequencies of unique haplotypes with -s specified
• .clustered_haplotype_frequency.txt The estimated frequencies of clustered haplotypes with -s and user specified haplotype clustering algorithm