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”).