title: LS05_ALL_presentation_WES
design: Germline DNA from cases LS09 and LS10 were extracted from formalin fixed paraffin embedded remission bone marrow using QIAamp DNA FFPE Tissue Kit (Qiagen). Other DNA samples were extracted from either bone marrow or peripheral blood using AllPrep DNA/RNA Mini Kit (Qiagen), QIAamp DNA Mini Kit (Qiagen), or innuPREP DNA/RNA Mini Kit (Analytik Jena), according to manufacturers instructions. The exons were captured using SureSelect XT2 Human All Exon V6 (Agilent), and sequenced by paired-end 75 bp sequencing on HiSeq4000 (Illumina), resulting in roughly 45 million reads per sample. Raw reads were aligned to human reference genome (hg19) using Burrows-Wheeler Aligner (BWA) 0.7.12 and were processed using the Genome Analysis Toolkit (GATK, v3.8) best practices recommended workflow for variant discovery analysis. MuTect (v1.1.7) and MuTect2 were used to identify somatic variants for each matched pair samples. Variants were annotated using Ensembl Variant Effect Predictor (VEP, version 90).