FindConventionalRecombinations

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

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REDHORSE Package

Example Data

Find Conventional Recombinations

REDHORSE employs a comparison based approach to scan potential recombinant loci using a fixed window and evaluates each potential break point by comparing it against other markers in the window and tags it based on the majority rule. It removes potential noisy loci and evaluates the breakpoints which sometimes form common boundaries of conventional recombinations as well as double crossovers and tags them appropriately.

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 conventional recombinations using findConventionalRecombinations utility of REDHORSE as follows:

java -jar REDHORSE.jar findConventionalRecombinations -i "PathToMergedAlleleFile" -j "PathToOutputFileWithAllRecombinations.txt" -k "PathtoOutputDirectoryWhereIndvRecombinationsAreWritten" -m 5 -n 9

-i is merged allele file
-j is the output file that contains locii where atleast one hybrid had a recombination
-k is the output directory where recombination information in each hybrid is reported individually
-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

Output

The output1 (-j) of the program is as follows:
Chromosome Position ref alt s1 s2 s3 s4 s5
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285 703053 A C A C A C C
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285 1579995 C A C A C C A
ref is the allele from reference genome, alt is the alternate allele, s1-s5 are the allele composition of each sample and pos is the position where recombination occurred

Index of Utilities
Analytical Pipeline