J LOH

Still the one from the block

What is JLOH?

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.

Warning

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.

What input does it need?

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

I have a hybrid, does it work with it?

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.