1 Next-Generation Sequencing, Variant Calling and Validation ... - PLOS
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1 Next-Generation Sequencing, Variant Calling and Validation ... - PLOS
Next-Generation Sequencing, Variant Calling and Validation WES was performed on germline genomic DNA extracted from peripheral-blood leukocytes of eligible patients. Exome enrichment was performed with the TruSeq SBS v.3 or Nextera Rapid Capture Exome (Illumina), and subsequent 100 bp paired-end sequencing was performed with Illumina HiSeq 2000 or 2500 platforms. Raw sequencing reads were mapped to the hg19 human reference haploid genome sequence using the Burrows-Wheeler Aligner (BWA version 0.6.1) [1]. Indel realignment, base and quality score recalibrations, and removal of PCR duplicates from the resultant Binary Alignment Map (BAM) files were performed using the Genome Analysis Toolkit (GATK) [2, 3], Sequence Alignment/Map (SAMtools) and Picard [4]. Variant discovery and genotype calling of single nucleotide variations (SNVs) and short insertions and deletions (indels,
