JLOH is a tool to extract, filter, and analyse loss of heterozygosity (LOH) blocks based on single-nucleotide polymorphisms (SNPs), read mapping information, and a reference genome sequence.
JLOH is made to assess LOH in genomes with at least 1% heterozygosity between their homolog chromosomes (or subgenomes, if hybrids). As of now, it isn't suitable for cancer data setups.
As of September 2023, this is just a landing page. Read the full documentation on jloh.readthedocs.io.
JLOH only needs three file types as input:
- VCF file with called heterozygous and homozygous SNPs
- BAM/SAM file with read mapping results, from which the variants were called
- FASTA file with a reference genome sequence where reads were mapped to get the BAM and VCF files
Yes, it does. The extraction module jloh extract can work with reads from a hybrid species mapped onto the hybrid's reference genome. See more about it on jloh.readthedocs.io.