生殖系
遗传学
种系突变
生物
计算生物学
假阳性悖论
鉴定(生物学)
统计的
序列(生物学)
突变
计算机科学
基因
人工智能
数学
统计
植物
作者
Daniel C. Koboldt,David E. Larson,Richard K. Wilson
标识
DOI:10.1002/0471250953.bi1504s44
摘要
The identification of small sequence variants remains a challenging but critical step in the analysis of next-generation sequencing data. Our variant calling tool, VarScan 2, employs heuristic and statistic thresholds based on user-defined criteria to call variants using SAMtools mpileup data as input. Here, we provide guidelines for generating that input, and describe protocols for using VarScan 2 to (1) identify germline variants in individual samples; (2) call somatic mutations, copy number alterations, and LOH events in tumor-normal pairs; and (3) identify germline variants, de novo mutations, and Mendelian inheritance errors in family trios. Further, we describe a strategy for variant filtering that removes likely false positives associated with common sequencing- and alignment-related artifacts.
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