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VariationAnalysis

Description Genetic variation analysis tools.
Component Version Inputs Outputs Description
Annovar 1.0 csvIn, vcfIn csvOut, vcfOut, analysis The component annotates genetic variants using ANNOVAR (table_annovar).
BreakpointVisualizer 0.1.1 cna, rearrangements report Visualizes genomic breakpoints resulting from copy-number aberrations (amplifications and deletions) and chromosomal rearrangements (translocations and inversions).
MutSig 1.0 variants, coverage, covariates genes, genesExcel Determine significantly mutated genes in a set of genetic variations using MutSig.
Summarization 1.0 data summarization Summarizes information from region using sliding window or group ids (same as SQL GROUP BY).
When sliding window is used, input file needs to be sorted according to locationCol Variation.jar is in microarray bundle.
VariantAnnotator 0.4 variantQuery, reference calls, log, raw This component is not being actively maintained currently, since Annovar is updated to frequently.
VariantCaller 1.0 reference, bam1, bam2, bams, intervals, dbsnp snp, indel, metrics

Calls genomic sites of variation using the specified caller.

VariantCombiner 1.0 reference, variants, variants1, variants2, variants3, variants4, variants5 calls This function combines all input variant files into one file using the Genome Analysis Toolkit (GATK).
VariantFilter 1.0 in, annotationArray, annotation out, alleleCount Filters variants based on allele frequencies in the data.
VariantLiftover 1.0 chain, oldReference, newReference, variants calls

This is analogous to the LiftOver component, but for VCF files.

VariantRecalibrator 1.0 reference, variants, hapmap, omni, hcsnp, dbsnp, mills calls This function will apply machine learning in order to improve the input variants.
VariantSelector 1.0 reference, variants, intervals, conc, disc calls Select variants from a VCF file using specific criteria, e.g. type, annotations or genomic intervals.
VariantValidator 1.0 reference, variants, dbsnp errors This function validates the input variant file using the Genome Analysis Toolkit (GATK).
VCF2CSV 1.0 vcf annotations, samples Converts variation calls in VCF format to CSV.
VCMM 0.1 pileup indel, snp, summary A variant caller, from VCMM website.

Generated 2019-01-14 07:42:05 by Anduril 2.0.0