DoubleCrossovers

REDHORSE- A Software Suite to Detect Recombinations From Next-Generation Sequencing Data

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ANALYTICAL PIPELINE

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SYSTEM REQUIREMENTS

REDHORSE Package

Example Data

Find double crossovers

The merged allele file which contains nucleotide information of parents as well as hybrids not only facilitates comparison of hybrids against the parents but also allows detection of double crossovers with reasonable accuracy because of presence of physical location of the markers. The recombination detection algorithm in REDHORSE employs an iterative procedure to find recombinations and double crossovers

Prerequisites

1) Generate Input Data
2) Find Alleles
3) List Alleles
4) Find SNVs
5) Filter SNVs in close proximity (optional)
6) Consolidate SNVs (optional)
7) Generate a merged allele file
8) Retain biallelic loci and filter out loci with lots of missing data (optional)

How to run it?

REDHORSE takes the merged allele file as input and finds double crossovers using findDoubleCrossovers utility of REDHORSE as follows:

java -jar REDHORSE.jar findDoubleCrossovers -i "Path2MergedAlleleFile" -o "outputDoubleCrossoversDetected" -m 5 -n 9 -p 5000 -q 5

-i is merged allele file
-o is the output file containing double crossovers
-m is the column number that contains allele information of parent 1 in merged allele file
-n is the column number that contains allele information of parent 2 in merged allele file
-p is the maximum size of the doublecrossover region
-q is the minimum number of markers supporting this doublecrossover region

Output

The output of the program is as follows:

sampleName Chromosome strt end numberofMarkers typeofSwitch
P1_29VBSF_GCTTAGA TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285 2716714 2717562 10 p1top2

sampleName is the name of the sample that had recombination, strt is the start position where double crossover started, end is the end position where double crossover ended, numberofMarkers is the number of markers supporting this region and typeofSwitch specifies if the hybrid switches from parent1 profile to parent2 profile or vice versa.

Index of Utilities
Analytical Pipeline