Calculate number of block-to-block junctions over the genome.
jloh junctions --blocks [<TSV> ...] [options]
--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.
--max-dist <INT>
Maximum distance between LOH blocks to consider them part of a candidate junction.