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Up: Category summary
Category
VariationAnalysis| Description | Genetic variation analysis tools. |
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| 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. |