ore 0.1.2

ORE: Outlier-RV enrichment
--------------------------

To use ORE (outlier-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
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

Felix Richter <felix.richter@icahn.mssm.edu>