ORE: Outlier-RV enrichment¶
Getting started¶
To use ORE (outlier-RV enrichment), confirm the following are installed:
Then, on the command line, install with pip using
pip install ore
Example run
1 2 3 4 5 6 7 8 | ore --vcf test.vcf.gz \
--bed test.bed.gz \
--output ore_results \
--distribution normal \
--threshold 2 3 4 \
--max_outliers_per_id 500 \
--af_rare 0.05 0.01 1e-3 \
--tss_dist 5000
|
Variants and gene expression are specified with --vcf
(line 1) and --bed
(line 2), respectively. The output prefix is provided with --output
(line 3). In this example, the outlier specifications --distribution
(line 4), --threshold
(line 5), and --max_outliers_per_id
(line 6) indicate that outliers are defined using a normal distribution with a z-score more extreme than two, and samples with more than 500 outliers are excluded. Variant information is specified with --af_rare
(line 7) and --tss_dist
(line 8) to encode that variants are defined as rare with a intra-cohort allele frequency at varying thresholds (≤ 0.05, 0.01, and 0.001), and to only use variants within 5 kb of the TSS.
Arguments¶
ore [-h] [--version] -v VCF -b BED [-o OUTPUT]
[--outlier_output OUTLIER_OUTPUT] [--enrich_file ENRICH_FILE]
[--extrema] [--distribution {normal,rank,custom}]
[--threshold [THRESHOLD [THRESHOLD ...]]]
[--max_outliers_per_id MAX_OUTLIERS_PER_ID]
[--af_rare [AF_RARE [AF_RARE ...]]] [--af_vcf]
[--intracohort_rare_ac INTRACOHORT_RARE_AC] [--gq GQ] [--dp DP]
[--aar AAR AAR] [--tss_dist [TSS_DIST [TSS_DIST ...]]] [--upstream]
[--downstream] [--annovar]
[--variant_class {intronic,intergenic,exonic,UTR5,UTR3,splicing,upstream,ncRNA,ncRNA_exonic}]
[--exon_class {nonsynonymous,intergenic,nonframeshift,frameshift,stopgain,stoploss}]
[--refgene] [--ensgene] [--annovar_dir ANNOVAR_DIR]
[--humandb_dir HUMANDB_DIR] [--processes PROCESSES] [--clean_run]
Contact¶
Please report bugs or requests through the Issue Tracker. Alternatively, contact Felix Richter at <felix.richter@icahn.mssm.edu>