Release notes - June 20, 2022
over 2 years ago by Marko Marinkovic
Data import from Gen3 BDC and Gen3 AnVIL available on BioData Catalyst powered by Seven Bridges
With this implementation, you are now able to bring data to BioData Catalyst powered by Seven Bridges after creating a cohort on BioData Catalyst powered by Gen3 or Gen3 Anvil. The process consists creating a cohort on Gen 3 Biodata Catalyst or Gen3 AnVIL, selecting and exporting data, connecting your account from one of the two external platforms to your account on the Platform, and finally importing the data into a controlled project on BioData Catalyst powered by Seven Bridges.
In addition, the import also includes the PFB file that was used as a manifest, as it contains all available data. Learn more.
Recently published apps
We have published three VarDict (v1.8.3, CWL1.2) tools and one workflow:
- VarDictJava is the VarDict variant caller Java port. It can be used to call SNPs, MNVs, small indels or complex variants from DNA or RNA alignments. VarDictJava can be used for amplicon-based variant calling and supports both single sample and paired sample analysis.
- VarDict var2vcf_valid, a CWL tool that takes VarDict variants tabular file and outputs variants in VCF format.
- VarDict var2vcf_paired, a CWL tool that converts VarDict tabular output to VCF.
- VarDict Variant Calling workflow (also VarDict v1.8.3, CWL1.2), which can be used for single sample and paired sample variant calling using VarDictJava starting from WES, WGS or amplicon data.
We have also published the following workflows and a toolkit:
- CNVnator Analysis workflow 0.4.1 for CNV calling by doing read-depth (RD) analysis of input BAM files.
- CNVpytor workflow 1.1 for CNV/CNA detection and analysis based on read depth and allele imbalance in WGS.
- PureCN workflow 1.22.0 for estimating tumor purity and ploidy, copy number and loss of heterozygosity (LOH) and PureCN NormalDB workflow which builds a normal database used for coverage normalization in PureCN workflow 1.22.0.
- FACETS workflow 0.6.1 for allele-specific copy number analysis (ASCN).
- Tabix BGZIP 1.14.0 for compressing/decompressing (BAM, VCF, BED, ...) any file in BGZF and from BGZF format and Tabix Index 1.14.0 which indexes a TAB-delimited genome position file IN.TAB.BGZ.