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).

A publication is available in the Computational and Structural Biotechnology Journal (Schiavinato et al., 2023).

Get started

• Installation
  • Docker
  • GitHub
• Quick start
  • Requirements
  • Calculating SNP density
  • Extracting blocks
• Run JLOH with a test dataset
  • Get LOH blocks
• Modelling SNP density
  • How to do it
  • Explanation
• Working with hybrids
  • Map hybrid reads onto parentals
  • Call variants
  • Run JLOH
  • Plot LOH blocks
• Working with cancer data
  • Remove secondary alignments
  • Call variants
  • Add allele frequency if missing
  • Infer LOH blocks in cancer datasets
• Hybrids with only one known parental

Extraction tools

• jloh stats
• jloh g2g
• jloh extract
• jloh onco_extract

Operations tools

• jloh filter
• jloh intersect
• jloh chimeric
• jloh junctions
• jloh cluster

Visualization tools

• jloh plot

Simulation tools

• jloh sim