ConsolidateSNVs

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

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SYSTEM REQUIREMENTS

REDHORSE Package

Example Data

Consolidate SNVs

Index 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)

How to run it?

This utillity consolidates two or more SNV files and finds SNVs that are specific to each SNV file and filters out SNVs that are common to two or more SNV files

java -jar REDHORSE.jar consolidateSNPs -i "C:\AsisKhan\softwareManuscript\data\filteredParentalSNPFiles" -o "C:\AsisKhan\softwareManuscript\data\consolidatedSNPFile\ConsolidatedSNPs.txt"

-i is the directory containing SNV files
-0 is the output consolidated file in VCF format

Output

The output of this utility is in the VCF format

Index of Utilities
Analytical Pipeline