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
.