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.

Marko Marinkovic