Whole-Genome Sequencing and Variant Analysis
Corresponding Organization :
Other organizations : Charité - Universitätsmedizin Berlin, Max Planck Institute for Molecular Genetics, Max Delbrück Center, Universitat Politècnica de Catalunya, Barcelona Supercomputing Center, German Cancer Research Center, Heidelberg University, University Hospital Cologne, University of Cologne, Berlin-Brandenburger Centrum für Regenerative Therapien, Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Variable analysis
- NucleoSpin Tissue kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany) for DNA extraction
- NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England BioLabs, Inc., Ipswich, MA) for library preparation
- Sequencing platforms: MGISEQ-2000 (NGP; MGI Tech Co. Ltd, Shenzhen, China), HiSeq X (IMR-5/75, Kelly; Illumina, Inc., San Diego, CA), and NovaSeq 6000 (CHP-212; Illumina, Inc., San Diego, CA) with 2 × 150 bp paired-end reads
- Quality control, adapter trimming, alignment, and duplicate removal as for ChIP-seq data
- Copy-number variation called using Control-FREEC (v11.4) with default parameters
- Structural variants called using SvABA (v1.1.1) in germline mode and discarding regions in a blacklist provided by SvABA
- Not explicitly mentioned
- No positive or negative controls were explicitly mentioned in the provided information.
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