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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