title: WXS fastq files from patient st096, Healthy tissue (blood)
design: Genomic DNA from fresh tumour samples was extracted using the DNeasy Blood and Tissue Kit (QIAGEN), following the manufacturers protocol; or the genomic DNA from the tumours was extracted from 2 m-thick FFPE sections (8-10 sections per sample) using Maxwell RSC DNA FFPE Kit (Promega Corporation) on Maxwell RSC 48 Instrument (Promega Corporation) following the manufacturers protocol. DNA from peripheral blood samples was used as a matching reference and extracted with the automatic QIAcube extractor (Qiagen), following the instructions of the DNeasy Blood & Tissue Kit (Qiagen). Whole exome was captured from genomic DNA for tumour and matched normal tissue using the SureSelectXT Human All Exon V6 + COSMIC (Agilent), following the manufacturers protocol. Somatic and germline variants were identified according to GATK Best Practices, implemented via the HaTSPiL framework. Sequencing reads were aligned to the GRCh37/hg19 reference genome using Novoalign (http://www.novocraft.com/) with default settings, allowing up to three mismatches per read. PCR duplicates were marked with Picards MarkDuplicates, and local realignment around indels was performed with GATKs RealignerTargetCreator and IndelRealigner.
library_name: Lib_207
identifiers.namespace: SUB15758673
identifiers.id: Lib_207