Hi-reComb

Estimating recombination maps from gamete Hi-C data

Author: Milan Malinsky Email: millanek@gmail.com

Quickstart:

Commands:
           FindInfoPairs       Find read pairs that would be informative for estimating the recombination
           RecombMap           Estimate the recombination map from informative Hi-C read pairs
Utilities:
           Simulate            Simulate informative read-pairs for a given map to evaluate confidence in reconstruction
           TrioPhase           Generate a phased het file for use with Hi-Recomb from a VCF with trio(s) (mother-father-offspring)

Usage:
1) samtools view ALIGNEMENT.bam | Hi-reComb FindInfoPairs [OPTIONS] HAPCUT2_PHASE.txt > INFORMATIVE_READS.sam
2) Hi-reComb RecombMap [OPTIONS] HAPCUT2_PHASE.txt INFORMATVE_PAIRS.sam

Utilities usage:
Hi-reComb Simulate [OPTIONS] ReferenceMap.txt INFORMATVE_PAIRS.sam
Hi-reComb TrioPhase [OPTIONS] OFFSPRING.vcf(.gz) PARENTS.vcf(.gz) PARENT1,PARENT2

Input files:

Required files:

All files should be divided by chromosome/scaffold.

1. An alignment file with Hi-C read pairs from gametes (sperm, pollen ...) from a single individual in the SAM / BAM format.
2. Phased SNPs at sites that are heterozygous in the donor (the individual from whom the gametes were obtained from). The phasing can be obtained directly from the Hi-C data using the hapcut2 software (make sure you use the --hic 1 option). Alternatively, if you have variant calls for the parents of the donor individual, you can use the Hi-reComb TrioPhase utility. In any case, the 'HAPCUT2_PHASE.txt' file should be in the hapcut2 format.

For suggestions/examples on obtaining the input data producing the input files see here.

Installation

To compile you must have a reasonably recent GCC (>=4.9.0) or clang compiler (on mac OS this comes with 'Command Line Tools').

$ git clone https://github.com/millanek/Hi-reComb
$ cd Hi-reComb
$ make

The Hi-reComb executable will be in the Build folder, so to run it type e.g. ./Build/Hi-reComb; this will show the available commands. To execute e.g. the RecombMap command, type ./Build/Hi-reComb RecombMap.