Associate outliers with rare variation
Project description
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 <felix.richter@icahn.mssm.edu>
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