{"title":"Release note 06.20.22","slug":"release-note-062022","body":"## Recently published apps\n\nWe have published three **VarDict** (v1.8.3, CWL1.2) tools and one workflow:\n* **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.\n* **VarDict var2vcf_valid**, a CWL tool that takes **VarDict** variants tabular file and outputs variants in VCF format.\n* **VarDict var2vcf_paired**, a CWL tool that converts **VarDict** tabular output to VCF.\n* **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.\n\nWe have also published the following workflows and a toolkit:\n* **CNVnator Analysis workflow 0.4.1** for CNV calling by doing read-depth (RD) analysis of input BAM files.\n* **CNVpytor workflow 1.1** for CNV/CNA detection and analysis based on read depth and allele imbalance in WGS.\n* **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**.\n* **FACETS workflow 0.6.1** for allele-specific copy number analysis (ASCN).\n* **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.","_id":"62b086dbc02f7001ecd88a27","changelog":[],"createdAt":"2022-06-20T14:40:27.394Z","user":{"name":"Marko Marinkovic","username":"","_id":"5767bc73bb15f40e00a28777"},"initVersion":{"version":"1.0","_id":"5773dcfc255e820e00e1cd50"},"project":"5773dcfc255e820e00e1cd4d","__v":0}

Release note 06.20.22


## 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.