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.
--dir
- directory--haplotypes
- FASTA with all haplotype sequences. Sequences needs to be namedmarker-id
f. ex. trap-1 all throughout the file.--marker
- name of the marker--indices
- comma separates ids for marker haplotypes
tmp.fasta
- FASTA with full sequences in marker haplotypestmp.snps
- FASTA with segregating SNPs in marker haplotypes
git clone https://github.com/juuzia/HapCheck.git
cd HapCheck
conda env create -n HapCheck --file env.yml
conda activate HapCheck
python HapCheck/get_haplotype_combinations.py --dir . --haplotypes <haplotype_file>.fasta --marker trap --indices 2,20,22,23,29,41,44,46