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

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 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>