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.