ore 0.1.5

Associate outliers with rare variation

To use ORE (outlier-RV enrichment), confirm the following are installed:

• python >=3.5.0

• bedtools >=2.27.0 (http://bedtools.readthedocs.io/en/latest/)

• samtools >=1.3 and bcftools >=1.6 (both from http://www.htslib.org/download/)

Then, on the command line, install with

pip install ore

Example run

ore --vcf test.vcf.gz \
    --bed test.bed.gz \
    --enrich_file enrichment.txt \
    --distribution "normal" \
    --threshold 2 3 4 \
    --max_outliers_per_id 500 \
    --af_rare 0.05 0.01 1e-3 \
    --tss_dist 5000

Usage, visit http://ore.readthedocs.io/en/latest/ for more

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 <[e-mail]>