Welcome to the JLOH documentation

What is JLOH?

JLOH (/jay’lo/) is a tool to extract, filter, and analyse loss of heterozygosity (LOH) blocks based on single-nucleotide polymorphisms (VCF), read mapping information (BAM), and a reference genome sequence (FASTA).

Get started:

• Installation
• Quick start
• Run JLOH with a test dataset
• LOH block extraction pipeline
• Working with hybrids

Modules description:

• jloh stats
• jloh g2g
• jloh extract
• jloh filter
• jloh intersect
• jloh cluster
• jloh chimeric
• jloh junctions
• jloh plot
• jloh sim