jloh filter

Description

Filter produced LOH blocks based on different criteria.

Usage

jloh filter --loh <LOH.tsv> [options]

Parameters

Input/Output

--loh <PATH>

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

Basic filters

--length <INT>

Minimum length (bp) of blocks to keep.

--alleles ["REF"|"ALT"|"NA"]

Allele annotation of blocks to keep. Multiple choices possible if space-separated (e.g. “REF NA”).

--zygosity ["homo"|"hemi"|"NA"]

Zygosity of blocks to keep. Multiple choices possible if space-separated (e.g. “hemi NA”).

--coverage <INT>

Minimum coverage of blocks to keep.

--region <STR>

Region where blocks must be kept, declared as chr:start-end, or simply chr.

SNP filters

--snps <INT>

Minimum number of SNPs found in block in order to keep it.

--het-snps <INT>

Minimum number of heterozygous SNPs found in block in order to keep it.

--homo-snps <INT>

Minimum number of homozygous SNPs found in block in order to keep it.

--snps-kbp <INT>

Minimum SNPs/kbp density found in block in order to keep it.

--het-snps-kbp <INT>

Minimum heterozygous SNPs/kbp density found in block in order to keep it.

--homo-snps-kbp <INT>

Minimum homozygous SNPs/kbp density found in block in order to keep it.