jloh intersect

Description

Perform intersection/removal operations with output files of jloh extract.

Usage

jloh intersect --loh-A <LOH_A.tsv> --loh-B <LOH_B.tsv> [options]

Parameters

Input / Output

--loh-A <PATH>

*.LOH_blocks.tsv output file produced by jloh extract.

--loh-B <PATH>

Another *.LOH_blocks.tsv output file produced by jloh extract.

Other options

--mode <STR>

What to do with the two input files. Choices are:

  • intersection (default): keep LOH blocks in common between the two files

  • complement: keep lines unique to --loh-A

  • unique: exclude common lines between the two files

--min-ovl <FLOAT>

Minimum overlap [0.0 - 1.0] between blocks to validate operation requested in --mode.