Associate outliers with rare variation
Project description
- To use ORE (utlier-RV enrichment), confirm the following are installed:
bedtools/2.27.0
samtools/1.3
bcftools/1.6
python/3.5.0
- Example run
ore –vcf test.vcf.gz –bed test.bed.gz –enrich_file enrichment.txt –distribution “normal” –threshold 2 –max_outliers_per_id 500 –af_rare 0.05 –tss_dist 5000
- Usage
- ore [-h] [–version] -v VCF -b BED [-o OUTPUT]
[–outlier_output OUTLIER_OUTPUT] [–enrich_file ENRICH_FILE] [–extrema] [–distribution {normal,rank,custom}] [–threshold THRESHOLD] [–max_outliers_per_id MAX_OUTLIERS_PER_ID] [–af_rare [AF_RARE [AF_RARE …]]] [–tss_dist [TSS_DIST [TSS_DIST …]]] [–upstream] [–downstream] [–annotations ANNOTATIONS] [–annovar] [–variant_class {intronic,intergenic,exonic,UTR5,UTR3,splicing,upstream,ncRNA}] [–annovar_dir ANNOVAR_DIR] [–humandb_dir HUMANDB_DIR] [–processes PROCESSES] [–clean_run]
Associate outliers with rare variants.
- Required arguments:
- -v VCF, --vcf VCF
Location of VCF file
- -b BED, --bed BED
Gene expression file location
- Optional file locations:
- -o OUTPUT, --output OUTPUT
Output prefix
- --outlier_output OUTLIER_OUTPUT
Outlier filename
- --enrich_file ENRICH_FILE
Output file for enrichment odds ratios and p-values
- Optional outlier arguments:
- --extrema
Only the most extreme value is an outlier
- --distribution DISTRIBUTION
Outlier distribution. Options: {normal,rank,custom}
- --threshold THRESHOLD
Expression threshold for defining outliers. Must be greater than 0 for –distribution normal or (0,0.5) non-inclusive with –distribution rank. Ignored with –distribution custom
- --max_outliers_per_id MAX_OUTLIERS_PER_ID
Maximum number of outliers per ID
- Optional variant-related arguments:
- --af_rare
AF cut-off below which a variantis considered rare
- --tss_dist
Variants within this distance of the TSS are considered
- --upstream
Only variants UPstream of TSS
- --downstream
Only variants DOWNstream of TSS
- --annotations ANNOTATIONS
Annotation file locations passed as a comma-separated list. Only variants in these annotations will be considered
- Optional arguments for using ANNOVAR:
- --annovar
Use ANNOVAR to specify allele frequencies and functional class ()
- --variant_class
- Only variants in these classes will be considered. Options:
{intronic,intergenic,exonic,UTR5,UTR3,splicing,upstream,ncRNA}
- --annovar_dir ANNOVAR_DIR
Directory of the table_annovar.pl script
- --humandb_dir HUMANDB_DIR
Directory of ANNOVAR data (refGene, ensGene, and gnomad_genome)
- optional arguments:
- -h, --help
show this help message and exit
- --version
show program’s version number and exit
- --processes PROCESSES
Number of CPU processes
- --clean_run
Delete temporary files from the previous run
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