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.

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