{"title":"Release note 06.06.22","slug":"release-note-060622","body":"## Data Cruncher and Interactive Analysis become Data Studio and Interactive Browsers\n\n**Data Studio**, previously **Data Cruncher**, is an interactive analysis tool which allows you to explore and visualize data using environments like JupyterLab and RStudio. Previously located under the **Interactive Analysis** tab, it has now been given a more prominent location in the project navigation by having its own tab located next to **Tasks**. With the removal of Data Studio from the **Interactive Analysis** tab, the tab's name has been changed to **Interactive Browsers** in order to better reflect its contents.\n\n## Recently published apps\n\nWe have just published an updated version (4.2.5.0) of **Mutect2** workflows:\n\n* **GATK Somatic SNVs and INDELs (Mutect2) 4.2.5.0**, a workflow used for somatic short variant calling. It runs on a single tumor-normal pair or on a single tumor sample, and performs additional filtering and functional annotation tasks, and\n* **GATK Create Mutect2 Panel of Normals 4.2.5.0** that creates a panel of normals for use in other GATK workflows. The workflow takes multiple normal sample callsets and passes them to **GATK Somatic SNVs and INDELs (Mutect2) 4.2.5.0** with tumor-only mode (although it is called tumor-only, normal samples are given as the input) and additionally collates sites present in two or more samples into a sites-only VCF.\n* Three apps from the MetaXcan toolkit:\n    * **S-PrediXcan** for computing associations between omic features and a complex trait starting from GWAS summary statistics.\n    * **S-MultiXcan** for computing association from predicted gene expression to a trait, using multiple studies for each gene.\n    * **MetaMany** for serially performing multiple MetaXcan runs on a GWAS study from summary statistics using multiple tissues.\n* The **MetaXcan** Workflow for computing associations between omic features and complex traits across multiple tissues. The workflow includes two tools from MetaXcan framework - **MetaMany** and **S-MultiXcan** and it uses summary statistics from a GWAS study and multiple models that predict the expression or splicing quantification.\n* **MaxQuant** (v2.0.3.0, CWL1.2), a quantitative proteomics tool designed for analysing large mass-spectrometric data. It uses a target-decoy search strategy to estimate and control the extent of false positives. Within the target-decoy strategy, **MaxQuant** applies the concept of posterior error probability (PEP) to integrate multiple peptide properties (e.g. length, charge, number of modifications) together with **Andromeda** score into a single quantity, reflecting the quality of a peptide spectrum match (PSM).\n* **Manta** (v1.6.0, CWL1.2), a tool used for calling structural variants (germline or somatic) from paired-end data. It can process WGS or WES data and supports germline SV calling on one or more samples (<=10) and somatic SV calling for matched tumor-normal pairs or tumor-only data.","_id":"629e20c077bb6f0073fb4a8a","changelog":[],"createdAt":"2022-06-06T15:44:00.558Z","user":{"name":"Marko Marinkovic","username":"","_id":"5767bc73bb15f40e00a28777"},"initVersion":{"version":"1.0","_id":"5773dcfc255e820e00e1cd50"},"project":"5773dcfc255e820e00e1cd4d","__v":0}

Release note 06.06.22


## Data Cruncher and Interactive Analysis become Data Studio and Interactive Browsers **Data Studio**, previously **Data Cruncher**, is an interactive analysis tool which allows you to explore and visualize data using environments like JupyterLab and RStudio. Previously located under the **Interactive Analysis** tab, it has now been given a more prominent location in the project navigation by having its own tab located next to **Tasks**. With the removal of Data Studio from the **Interactive Analysis** tab, the tab's name has been changed to **Interactive Browsers** in order to better reflect its contents. ## Recently published apps We have just published an updated version (4.2.5.0) of **Mutect2** workflows: * **GATK Somatic SNVs and INDELs (Mutect2) 4.2.5.0**, a workflow used for somatic short variant calling. It runs on a single tumor-normal pair or on a single tumor sample, and performs additional filtering and functional annotation tasks, and * **GATK Create Mutect2 Panel of Normals 4.2.5.0** that creates a panel of normals for use in other GATK workflows. The workflow takes multiple normal sample callsets and passes them to **GATK Somatic SNVs and INDELs (Mutect2) 4.2.5.0** with tumor-only mode (although it is called tumor-only, normal samples are given as the input) and additionally collates sites present in two or more samples into a sites-only VCF. * Three apps from the MetaXcan toolkit: * **S-PrediXcan** for computing associations between omic features and a complex trait starting from GWAS summary statistics. * **S-MultiXcan** for computing association from predicted gene expression to a trait, using multiple studies for each gene. * **MetaMany** for serially performing multiple MetaXcan runs on a GWAS study from summary statistics using multiple tissues. * The **MetaXcan** Workflow for computing associations between omic features and complex traits across multiple tissues. The workflow includes two tools from MetaXcan framework - **MetaMany** and **S-MultiXcan** and it uses summary statistics from a GWAS study and multiple models that predict the expression or splicing quantification. * **MaxQuant** (v2.0.3.0, CWL1.2), a quantitative proteomics tool designed for analysing large mass-spectrometric data. It uses a target-decoy search strategy to estimate and control the extent of false positives. Within the target-decoy strategy, **MaxQuant** applies the concept of posterior error probability (PEP) to integrate multiple peptide properties (e.g. length, charge, number of modifications) together with **Andromeda** score into a single quantity, reflecting the quality of a peptide spectrum match (PSM). * **Manta** (v1.6.0, CWL1.2), a tool used for calling structural variants (germline or somatic) from paired-end data. It can process WGS or WES data and supports germline SV calling on one or more samples (<=10) and somatic SV calling for matched tumor-normal pairs or tumor-only data.