Up: Components summary
Up: Components summary
Author
Rony Lindell| Component | Version | Inputs | Outputs | Description |
|---|---|---|---|---|
| BamReducer | 1.0 | reference, bam | alignment | This function reduces the reads in a bam file using the Genome Analysis Toolkit (GATK) 2 and outputs a dramatically more compressed bam file. |
| BamRegrouper | 1.0 | bam | alignment | Picard-tools is used to add or replace read group information for each read in the input alignment file. |
| BamReorder | 1.0 | reference, bam | alignment | This function reorders reads in a BAM file to match the contig ordering in the provided reference file. . |
| BaseRecalibrator | 1.0 | reference, bam, dbsnp, mask, intervals | alignment, report, plots | This function will do base quality score recalibration using Genome Analysis Toolkit (GATK). |
| DuplicateMarker | 2.0 | in | outBam, outMetrics | Mark PCR and optical duplicate reads in BAM files using Picard MarkDuplicates. |
| ReferenceIndexer | 1.0 | reference | index | The following auxiliary files for the reference fasta sequence will be created:
|
| Sam2Fastq | 1.0 | alignment | folder, reads, mate | This function uses the Picard java library to perform a conversion from SAM/BAM alignment format back to FASTQ sequence format. |
| 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). |
| 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). |