StandardizeMergedAllele

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

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Standardize Merged Allele file

REDHORSE takes a merged allele file and using a window size of 10 markers and step size of 1 marker, averages the observations in a window. The utility verifies if majority of alleles in a window look like parent 1 or parent 2 and then writes it to an output file.

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 as input and standardizes it using the utility StandardizeMergedAlleleFile

java -jar REDHORSE.jar StandardizeMergedAlleleFile -i mergedAlleleFile -j outputStandardizedFile -m parent1Column -n parent2Column -k WindowSize

-i is merged allele file
-j is the standardized mergedAlleleFile
-k is the window size
-m is the column number that contains allele information of parent 1 in merged allele file
-n is the column number that contains allele information of parent 2 in merged allele file

Output

The output1 (-j) of the program is as follows:
chr    pos    ref    parent    ME49Parental_filtered.list    P1_29VBSF_GCTTAGA.list    P1_39VB_AGACTGA.list    P1_45VB_AGACTGA.list    VAND_filtered.list
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285    2095    C1    C2    C1    C2    C1    C1    C2
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285    2192    C1    C2    C1    C2    C1    C1    C2
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285    2577    C1    C2    C1    C2    C1    C1    C2
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285    2860    C1    C2    C1    C2    C1    C1    C2
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285    3780    C1    C2    C1    C2    C1    C1    C2
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285    3997    C1    C2    C1    C2    C1    C1    C2
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285    4142    C1    C2    C1    C2    C1    C1    C2
.....
.....

The program replaces the base composition information with "C1" if the window of 10 bp contains alleles similar to parent1 and with "C2" if the alleles are similar to parent2.

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