Below is a list of the tools in DISCVR-seq Toolkit. Tools in the 'Public' category are intended to be more general-purpose, include more extensive automated testing, and should be stable. Tools in the 'Development' section may be subject to change and have potentially received less testing.
Unlike the public tools group, these tools may have have received less rigorous testing and may be under active development.
| Name | Summary |
|---|---|
| ImmunoGenotyper | Provides genotyping summary for complex multigenic loci, like KIR or MHC. |
| PrintReadBackedHaplotypes | Reconstructs and prints a list of distinct read-backed sequences over the supplied intervals |
These tools should be rigorously validated and stable.
| Name | Summary |
|---|---|
| ExtendedFuncotator | Functional Annotator |
| IdentifySoftClippedLoci | Generate a list of loci with three or more distinct bases detected |
| IntegrationSiteMapper | Detect and summarize transgene integration |
| MergeFastqReads | Merges paired FASTQ reads into a single read |
| MultipleAllelesAtLoci | Generate a list of loci with three or more distinct bases detected |
| PrintReadsContaining | Print read pairs matching a list of sequences/expressions |
| SplitVcfBySamples | Splits a VCF into multiple VCFs based on samples |
| VcfToLuceneIndexer | Index a VCF using Apache Lucene |
These tools are designed for fairly specialized purposes and are most likely only useful internally.
| Name | Summary |
|---|---|
| AnnotateNovelSites | Annotates a VCF based on whether sites are present in a reference VCF |
| BackportLiftedVcf | Backport lifted VCF to the original coordinates |
| ClinvarAnnotator | Annotate variants overlapping ClinVar |
| ClipOverlappingAlignments | Clip alignments overlapping the specified intervals |
| FindGenomeDifferences | Create VCF summarizing positions where reference alleles differ between genomes |
| GroupCompare | Produce a list of candidate variants based on a sample list |
| MultiSourceAnnotator | Transfers annotations from ClinvarAnnotator and Cassandra VCFs to a source VCF |
| OutputVariantsStartingInIntervals | Output only variants starting within the provided intervals |
| Summarize10xAlignments | Iterate a 10x BAM and summarize alignments per gene |
| VariantConcordanceScore | Summarize allele-level concordance between a VCF and reference VCFs |
| VcfFilterComparison | Summarize filtering between two VCFs |
These tools perform manipulation/QC of variant data, and should be rigorously validated and stable.
| Name | Summary |
|---|---|
| AppendGenotypes | Merge multiple VCFs to produce one with all sites |
| CrossSampleGenotypeComparison | Produces a concordance report between samples in a VCF against every other sample in a reference VCF |
| DiscvrVariantAnnotator | Tool for adding annotations to VCF files |
| GenotypeFilterBySample | Filters genotypes based on an input list of samples/sites |
| MergeVariantSites | Merge multiple VCFs to produce one with all unique sites |
| MergeVcfsAndGenotypes | Generate a merged VCF from one or more inputs |
| RemoveAnnotations | Iterate a VCF and selectively remove annotations using using a whitelist or blacklist |
| SampleSpecificGenotypeFiltration | Allows filtration of genotypes with sample-specific expressions |
| VariantQC | Generate HTML summary report for a VCF |
| VcfComparison | Produces a concordance report between two VCFs at the site and genotype level |
See also General Documentation | Tool Docs Index Tool Docs Index | Issues/Help
DISCVR-Seq version 1.3.78 built at 02-11-2024 02:17:36.