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.
- C++ (at least GCC 5)
- GNU Make
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: ./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.