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The sequenced reads in the FASTQ files were aligned to the human genome assembly (hg19) using the Burrows-Wheeler aligner (BWA). The initial alignment BAM files were subjected to sorting (SAMtools), removing duplicated reads (Picard), locally realigning reads around potential small insertion/deletion and recalibrating base quality score [Genome Analysis Toolkit (GATK)]. We used MuTect to generate high-confidence predictions on mutation calls. Variant Effector Predictor was used to annotate the called mutations.
Copyright and License information: ©2019 Lim, Sa, Lee, Kim, Kim, Park, Ku, Park, Park, Lim, Kang, Nam and Lee.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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