Up: Components summary
Up: Components summary
Author
Amjad Alkodsi| Component | Version | Inputs | Outputs | Description |
|---|---|---|---|---|
| Align | 1.0 | reads, mates, reference | out | This component aligns sequencing reads to the reference genome using the Borrows-Wheeler aligner with the mem algorithm. Complete documentation: . |
| Annovar | 1.0 | csvIn, vcfIn | csvOut, vcfOut, analysis | The component annotates genetic variants using ANNOVAR (table_annovar). |
| Ascat | 1.3 | tumorLogR, tumorBAF, controlLogR, controlBAF, gcContent, gender | results, summary, intermediate, plots | Runs Allele specific copy number analysis with ploidy and tumor purity estimation using the tool ASCAT. |
| BamCombiner | 2.0 | in | out | Merges multiple bam files using the Picard MergeSamFiles. |
| BamStats | 1.0 | bam, refGenome, targets, chrLength, markStats | report, summary | The function collects alignment and coverage statistics from a bam file. |
| BICseq | 1.0 | test, control | results, calls, cloneCalls | Detects copy number alterations from whole-genome sequencing data using BICseq
tool. |
| BismarkAlign | 1.0 | reads, refGenome, mates | methylationCalls, bedGraph, alignment, Mbias, report, analysis | Performs alignment of bisulfite sequencing data in addition to deduplication
and methylation extraction using Bismark Bisulfite Mapper. |
| CSVDplyr | 1.2 | csv1, csv2, csv3, in | out | Applies up to R functions (including dplyr functions) to the input csv1. |
| GenomeSlider | 1.0 | matrix, regions, chrLengths | regionsSummary, windowsSummary | Summarized genomic events at sliding window intervals and/or at predifined regions. |
| HeatMapReport | 3.0 | in, rowLabels, colLabels | out | Clusters samples hierarchically and draws the corresponding dendrograms and heat map. |
| KaplanMeierPlot | 1.0 | in | plots, plotObject, survPvalue, CoxStats | Plots Kaplan Meier survival plot using the survival and survminer R packages. |
| MethylExtract | 1.0 | bam, refGenome | CpGmeth, CHGmeth, CHHmeth, SNVs, analysis | Extracts methylation from a bam file simultaneously with variant calling. |
| PrepRnaBam | 1.0 | reference, in, dbsnp, mask | alignment, markReport, recalReport | Preprocessing of RNA bam files according to GATK best practices (adding groups, marking duplicates, splitNtrim and base recalibration). |
| Realigner | 1.0 | reference, bam1, bam2, knownTargets, indels1, indels2, indels3, intervals | realignedCase, realignedControl, targets | This function will do local realignment around indels using Genome Analysis Toolkit (GATK). Complete documentation: . |
| RNAVariantCaller | 1.0 | reference, in | out | Variant calling in RNAseq data using HaplotypeCaller and VariantFiltration in GATK. |
| SignatureExtractor | 1.2 | in | outContribution, outNmuation, signatureDistance, plots | This component performs signature extraction from point mutation data using non-negative matrix factorization following the pipeline in SomaticSignature R package. |
| TrimGalore | 1.1 | reads, mates | trimmed, report, stats | The component is a wrapper of the trim_galore tool which is also a
wrapper of two tools: fastqc and cutadapt which both should
be in PATH. |