PMC:4385186 / 7289-8802 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4385186","sourcedb":"PMC","sourceid":"4385186","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4385186","text":"Mutation Detection\nFor detection of somatic point mutations, sequencing reads from a Illumina HiSeq 2000 were aligned to the human reference genome (UCSC Genome Browser hg19) with the Burrows-Wheeler Aligner. After duplicate reads (redundant information produced by PCR) were removed with SAMtools, an in-house pipeline was used to call somatic mutations. In brief, we implemented SAMtools (v.0.1.18) and VarScan (v.2.2.5) to call somatic variants. We required a minimum depth of 10× and variant frequency of 10% for both normal and tumor samples in order to call a specific variant at that locus. A single-nucleotide variant (SNV) was labeled highly confident if it met the following requirements: (1) the locus was not enriched with reads of low mapping quality, (2) reads that supported the SNV were not significantly overrepresented with bases of low quality, (3) reads that supported the SNV showed no bias toward the read end, (4) no gaps were found near the SNV locus, and (5) the SNV was not encompassed in short repeat regions.\nThe indel-calling step was performed by the Genome Analysis Toolkit SomaticIndel Detector with default parameters. The highly confident indels were identified by an in-house pipeline and further annotated as germline or somatic on the basis of whether any evidence of the event at the same locus was observed in the normal data. Finally, highly confident SNVs were annotated with ANNOVAR and used in follow-up analysis. A full list of mutation events is presented in Table S3.","divisions":[{"label":"title","span":{"begin":0,"end":18}},{"label":"p","span":{"begin":19,"end":1036}}],"tracks":[]}