Package: ore
Cursory use of ORE (outlier-RV enrichment) is provided here, visit thelatest ORE documentationfor more details. Confirm the following are installed:Python >=3.5.0bedtools >=2.27.0samtools >=1.3 and bcftools >=1.6Then, on the command line, install withpip install oreExample runore--vcftest.vcf.gz\--bedtest.bed.gz\--outputore_results\--distributionnormal\--threshold234\--max_outliers_per_id500\--af_rare0.050.011e-3\--tss_dist5000Variants 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.Usage, visit thelatest ORE documentationfor moreore [-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]Required arguments:-vVCF,--vcfVCFLocation of VCF file. Must be tabixed!-bBED,--bedBEDGene expression file location. Must be tabixed!Optional file locations:-oOUTPUT,--outputOUTPUTOutput prefix (default is VCF prefix)--outlier_outputOUTLIER_OUTPUTOutlier filename (default is VCF prefix)--enrich_fileENRICH_FILEOutput file for enrichment odds ratios and p-values (default is VCF prefix)Optional outlier arguments:--extremaOnly the most extreme value is an outlier--distributionDISTRIBUTIONOutlier distribution. Options:
{normal,rank,custom}--thresholdTHRESHOLDExpression threshold for defining outliers. Must be
greater than 0 for normal or (0,0.5)
non-inclusive with rank. Ignored with custom--max_outliers_per_idMAX_OUTLIERS_PER_IDMaximum number of outliers per IDOptional variant-related arguments:--af_rareAF_RAREAF cut-off below which a variant is considered rare (space separated list e.g., 0.1 0.05)--af_vcfUse the VCF AF field to define an allele as rare.--intracohort_rare_acINTRACOHORT_RARE_ACAllele COUNT to be used instead of intra-cohort allele
frequency. (still uses af_rare for population level AF
cut-off)--af_minAF_MINLower bound on AF cut-offs for –af_rare, must be same
length as –af_rare (e.g., with –af_rare 0.01 0.5 and
–af_min 0 0.05 ORE will compare variants within
[0,0.01] and [0.05,0.5] to other variants).--gqGQMinimum genotype quality each variant in each individual--dpDPMinimum depth per variant in each individual--aarAARAlternate allelic ratio for heterozygous variants
(provide two space-separated numbers between 0 and 1,
e.g., 0.2 0.8)--tss_distTSS_DISTVariants within this distance of the TSS are
considered--upstreamOnly variants UPstream of TSS--downstreamOnly variants DOWNstream of TSSOptional arguments for using ANNOVAR:--annovarUse ANNOVAR to specify allele frequencies and
functional class--variant_classOnly variants in these classes will be considered. Options:
{intronic,intergenic,exonic,UTR5,UTR3,splicing,upstream,ncRNA}--exon_classOnly variants with these exonic impacts will be
considered. Options:
{nonsynonymous,intergenic,nonframeshift,frameshift,stopgain,stoploss}--refgeneFilter on RefGene function.--ensgeneFilter on ENSEMBL function.--annovar_dirANNOVAR_DIRDirectory of the table_annovar.pl script--humandb_dirHUMANDB_DIRDirectory of ANNOVAR data (refGene, ensGene, and
gnomad_genome)optional arguments:-h,--helpshow this help message and exit--versionshow program’s version number and exit--processesPROCESSESNumber of CPU processes--clean_runDelete temporary files from the previous runFelix Richter <felix.richter@icahn.mssm.edu>