jloh junctions

Description

Calculate number of block-to-block junctions over the genome.

Usage

jloh junctions --blocks [<TSV> ...] [options]

Parameters

Input / Output

--blocks <PATH> | [<PATH_1> <PATH_2>]

This input parameter works in two different ways, both with *.LOH_blocks.tsv files produced by jloh extract.

  • one input file: Junctions are searched within the file between blocks of different alleles (REF, ALT).

  • two input files: Junctions are searched between the two files.

--gff <PATH>

GFF file containing gene models that will be used to produce more in-depth statistics in the output.

--genome <PATH>

FASTA file with the genome sequence where blocks were called.

Other options

--max-dist <INT>

Maximum distance between LOH blocks to consider them part of a candidate junction.