Release note 03.28.22

Recently published apps

New apps have been added to CAVATICA:

Two tools from the Samplot toolkit:

  • Samplot Plot takes alignment files and coordinates for a region containing the SV call of interest (Chromosome, Start position, and End position) and creates a plot of the SV region.
  • Samplot Vcf can be used to create visualizations of structural variant calls from a VCF file.

Seven tools from the Smoove toolkit:

  • Smoove Annotate annotates SV calls with SV quality and gene information from GFF3 files.
  • Smoove Call calls structural variants with Lumpy and optionally calls svtyper.
  • Smoove Duphold annotates SV calls in the file based on information from the provided alignment files.
  • Smoove Genotype runs svtyper in parallel on provided SV inputs.
  • Smoove Merge merges SV calls from individual files with SV calls and sorts them using svtools.
  • Smoove Paste squares matching SV calls from individual files to a single joint file with final calls.
  • Smoove Plot-counts takes a VCF file created by other Smoove tools and plots counts of split and discordant reads before and after filtering.

Upgraded four Sambamba tools to 0.8.1 (and CWL 1.2) and added three new tools:

  • Sambamba Flagstat generates statistics from read flags in a BAM file.

  • Sambamba Index creates a BAI or FAI index for the provided input.

  • Sambamba Markdup can be used to mark or remove duplicate reads from an input BAM file.

  • Sambamba Merge merges alignments in BAM format.

  • Sambamba Slice can be used to copy a slice (region) of the coordinate sorted and indexed input file in BAM or FASTA format.

  • Sambamba Sort sorts alignments in BAM format.

  • Sambamba View accepts alignments in BAM or SAM format and outputs data in a user-specified format.

  • Vcf2maf is a tool that converts VCF files to MAF files. To obtain a MAF file from a VCF, each variant must be mapped to exactly one gene transcript/isoform that it might affect, and be associated with exactly one effect. Vcf2maf invokes Variant Effect Predictor to choose the transcript and effect associated with each variant in the output MAF file.

  • Cancer Predisposition Sequencing Reporter tool that can be used to interpret germline variants in the context of cancer predisposition. The tool takes a VCF file with germline variants obtained from WES or WGS, cross-references the set with the user-selected set of genes of interest, annotates the variants and reports the associated information (ClinVar-classified variants, ACMG secondary findings, Variant biomarkers and GWAS hits).

  • Personal Cancer Genome Reporter can be used to analyze a VCF with somatic variants obtained using WES, WGS or targeted sequencing. It is a tool for functional annotation and classification of somatic variants.

  • Whole Genome Sequencing - Quality Control workflow, used for quality control of WGS data. The workflow is intended as a general-purpose QC workflow for users processing WGS data, offering plots which can be easily inspected, as well as structured data output suitable for aggregation and parsing in an automated setup (JSON and TAR.GZ archive with all QC files).