MergedAlleleFile

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

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REDHORSE Package

Example Data

Generate a Merged Allele File

REDHORSE takes the consolidated SNV file and finds the allele composition from all the hybrids at those variant loci. This master file containing the allele composition of the parents as well as the hybrids and their actual marker positions in the genome can be used to infer the recombinations and double crossovers in each hybrid.

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)

How to run it?

This utillity summarizes the allele information from all the samples at the loci indicated

java -jar REDHORSE.jar findMergedAlleles -i "C:\AsisKhan\softwareManuscript\data\ListFiles" -j "C:\AsisKhan\softwareManuscript\data\consolidatedSNPFile" -o "C:\AsisKhan\softwareManuscript\data\mergedAllele.txt" -k "VCF"

-i is the directory containing List files
-j is the directory containing snv Files or filtered snv files or consolidated file
-0 is the output merged allele file containing allele information from all samples in -i at loci specified by SNV file(s) in -j
-k is the format of the files in the snp directory specified in -j

Output

The output of the program is as follows:

chr    pos    ref    parent    list1.list    list2.list
TGME49_chrXII   4167    G    T    T    G
TGME49_chrXII   4494    A    G    G
TGME49_chrXII   4670    T    A    -    T
TGME49_chrXII   5858    A    C    C    A
TGME49_chrXII   6146    C    T    -    C
TGME49_chrXII   6461    G    C    -    -
TGME49_chrXII   6706    A    G    G    A
TGME49_chrXII   6766    G    A    A    G
TGME49_chrXII   7135    C    T    -    C
.....
.......
........

Column 1 is the chromosome name, column 2 is the genomic position, column 3 is the reference allele/allele from control sample, column 4 is the allele from the other parent, column 5 and further are the alleles from the sequenced hybrids. In this example, there are two hybrids whose information is incorporated into the merged SNP file. If the hybrid files have no information because of the insufficient read depth at that location, the missing data is reported using a "-".

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