Metadata-Version: 1.2
Name: ore
Version: 0.1.1
Summary: Associate outliers with rare variation
Home-page: http://github.com/frichter/ore
Author: Felix Richter
Author-email: felix.richter@icahn.mssm.edu
License: MIT
Description-Content-Type: UNKNOWN
Description: ORE: Outlier-RV enrichment
        --------------------------
        
        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
        
        
        
Keywords: rnaseq,wgs,outliers,rare_variants,rna,dna
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3
