HapCheck

Inspect final marker haplotypes. Identify which haplotypes might be redundant/chimeric and are created from fragments of other two marker haplotypes. Comparisons are done for each pair.

Input

• --dir - directory
• --haplotypes - FASTA with all haplotype sequences. Sequences needs to be named marker-id f. ex. trap-1 all throughout the file.
• --marker - name of the marker
• --indices - comma separates ids for marker haplotypes

Output

• tmp.fasta - FASTA with full sequences in marker haplotypes
• tmp.snps - FASTA with segregating SNPs in marker haplotypes

example.jpg

Set-up

Clone repository

git clone https://github.com/juuzia/HapCheck.git

Create conda environment

cd HapCheck
conda env create -n HapCheck --file env.yml
conda activate HapCheck

Example usage

python HapCheck/get_haplotype_combinations.py --dir . --haplotypes <haplotype_file>.fasta --marker trap --indices 2,20,22,23,29,41,44,46