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SearchBackupMarkers

SearchBackupMarkers is for selecting additional informative, highly polymorphic markers to an existing set of markers. Useful in replacing poor quality markers in a marker set.

Requirements

Need Java 13 or newer. Check if you have Java, otherwise you can install it from here.

Installation

Through git clone

git clone https://jcignacio@bitbucket.org/jcignacio/purity.git

Then go to the directory

purity/builds/SearchBackupMarkers_220110

OR

Download it from SearchBackupMarkers_220110.zip then extract.

Run test data

java -jar sbm.jar 5 1000 0.0 files/file_to_choose_from.hmp.txt out.txt files/file_to_backup.hmp.txt

Usage

java -jar sbm.jar <Number of target markers> <Population size> <Distance bet. duplicate samples> <Input HapMap file> <Output file> <file to backup> <optional: start pos>

Parameters	Description
Number of target markers, N (integer)	number of markers to select/add
Popoulation size (integer)	number of solutions to consider at a time (better results when higher but uses more RAM)
Distance bet. duplicate samples (decimal, 0 to 1)	genetic distance threshold for considering duplicated samples, set to 0 for exact match. Set higher for more polymorphic markers between samples.
Input hmp.txt (file)	hapmap file where to pick markers from
Output file (file)	output file, e.g. out.txt
File to backup (file)	hapmap file containing existing markers (selected, validated or working markers). Must contain the same exact samples as the input hmp file.
Start pos (integer)	optional, skip first n markers in File to backup

Results and outputs	Description
Score ([m1,m2,..mN --> x])	the score (x) denotes the number of unique genotypes
Text file	contains some information on the selected markers
Hapmap file	subset of the input hapmap file containing the selected markers only