FastRecomb

FastRecomb is an efficient tool to infer recombination rates using a biobank-scale haplotype panel. We recommend using P-smoother before running FastRecomb, specifically for panels with medium to high genotyping error rates (e.g. > 0.1%). The input file format for FastRecomb is (phased) VCF.

Dependencies

• C++ (at least GCC 5)
• GNU Make

Installation

To install the program clone the repository to a local folder using:

git clone https://github.com/ZhiGroup/FastRecomb.git

Enter the Debug folder and compile the program:

cd FastRecomb/Debug
make

Usage:

<pre> Usage: ./FastRecomb -i [vcf_file] -o [output_folder] -L [genetic_length_cM_total] -d [min_length] -r [num_iterations] -w [window_size] Required parameters: -i [vcf_file] Path to the VCF input file. -o [output_folder] Output file will be written in output_folder including any intermediate file. -L [genetic_length_cM_total] The expected total length of the chromosome in cM. Optional parameters: -d [min_length] Minimum genetic length of the haplotype matches. The minium length is 0.5 cM by default. -r [num_iterations] Number of iterations. The values is set to 5 by default. -w [window_size] Window size in bps. It is set to 5000 by default. A recombination rate is calculated for each window across the chromosome. </pre>