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




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SYSTEM REQUIREMENTS

REDHORSE Package  

Example Data
Retain Bi-allelic segments and filter out multi-alleleic segmentsIndex of Utilities
Analytical Pipeline

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

How to run it?

REDHORSE takes the merged allele file and filters out loci where there are more than 2 alleles

java -jar REDHORSE.jar keepBiallelicSegments -i "C:\AsisKhan\softwareManuscript\data\mergedAllele.txt" -o "C:\AsisKhan\softwareManuscript\data\mergedAllele_1.txt"

-i is merged allele file
-0 is the output filtered merged allele file

Output

The output of the program is same as that of a merged allele file




Index of Utilities
Analytical Pipeline