FilterMissingDataLoci

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

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ANALYTICAL PIPELINE

CONTACT

SYSTEM REQUIREMENTS

REDHORSE Package

Example Data

Filter loci where more than x% of samples have missing data

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 x% of missing data

java -jar REDHORSE.jar filterMergedSNPFile4MissingData -i "C:\AsisKhan\softwareManuscript\data\mergedAllele_1.txt" -m 30 -o "C:\AsisKhan\softwareManuscript\data\mergedAllele_2.txt"

-i is merged allele file
-m is the percentage of missing data (anything greater than that % is filtered out). In the above example, loci with more than 30% of samples having missing data are filtered out
-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