jloh chimeric

Description

This module extracts genes from a genome annotation file which contain traces of LOH towards two different haplotypes (REF and ALT).

Biologically, these are likely the result of an LOH breakpoint placed within an intron of a gene, so that part of the gene has the REF haplotype, and part of the gene has the ALT one.

Usage

jloh chimeric --blocks-A <TSV> --blocks-B <TSV> --het <BED> --gff <GFF> [options]

Parameters

--blocks-A <PATH>

A TSV file produced by jloh extract.

--blocks-B <PATH>

Another TSV file produced by another run of jloh extract, profiling a different genotype from --blocks-A.

--het <PATH>

Heterozygous regions identified by jloh extract.

If the extraction was done with --assign-blocks it has produced two files with Heterozygous blocks (one per parental genome). In that case, concatenate them together.

--gff <PATH>

GFF3 file containing gene models from the reference FASTA file used to infer LOH blocks.

--out-prefix <PATH/STR>

Pre-pend this prefix to each output file (path allowed).

--quiet <BOOL>

Suppress warnings.

--feature <STR>

What feature to look for (see GFF format, 3rd column). Examples are “gene”, “exon”, “CDS”, “mRNA”.

--min-overlap <FLOAT>

Minimum fraction [0.0 - 1.0] of a feature that must overlap an LOH block to create an instance of candidate chimeric feature.

--id-attr <STR>

Attribute to search for to get the names of the features analysed (GFF3 last column, e.g. “ID”).