BlackOPs: increasing confidence in variant detection through mappability filtering.
BlackOPs: increasing confidence in variant detection through mappability filtering.
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DOI：
10.1093/nar/gkt692
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发表时间：
2013-10
影响因子：
14.9
通讯作者：
Hayes DN
中科院分区：
文献类型：
--
作者：
Cabanski CR;Wilkerson MD;Soloway M;Parker JS;Liu J;Prins JF;Marron JS;Perou CM;Hayes DN
使用高通量测序数据识别变种目前是一个挑战，因为真正的生物变种可能与技术制品难以区分。技术伪影的一个来源是不正确地将实验观察到的序列与其真实的基因组起源(错误映射)进行比对，并将错误映射的序列中的差异推断为真实的变体。我们开发了BlackOps，这是一个开源工具，模拟了来自参考基因组的实验RNA-seq和DNA整个外显子组序列，通过定制参数对这些序列进行比对，检测变异并输出错误映射导致的位置和等位基因黑名单。黑名单包含数以千计的人工产物变体，这些变体与真实变体难以区分，对于给定的样本，预计几乎完全是假阳性。我们表明，这些黑名单位置特定于所使用的比对算法和读取长度，并且BlackOps允许用户生成特定于其实验设置的黑名单。我们查询了DBSNP和COSMIC VARIANT数据库，发现了许多无法与映射错误区分的变体。我们使用RNA-seq胶质母细胞瘤细胞系数据集展示了过滤黑名单位置如何减少潜在虚假变异的数量。总而言之，考虑到调整到实验设置的图谱引起的变体减少了假阳性，因此，通过高通量测序改善了基因组特征。
Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.
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影响因子：
158.5
作者：
Lynch, TJ;Bell, DW;Haber, DA
通讯作者：
Haber, DA
影响因子：
12.3
作者：
Cirulli ET;Singh A;Shianna KV;Ge D;Smith JP;Maia JM;Heinzen EL;Goedert JJ;Goldstein DB;Center for HIV/AIDS Vaccine Immunology (CHAVI)
通讯作者：
Center for HIV/AIDS Vaccine Immunology (CHAVI)
基因组暗物质：基因组映射分数所说明的简读映射的可靠性。
DOI：
10.1093/bioinformatics/bts330
发表时间：
2012-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lee H;Schatz MC
通讯作者：
Schatz MC
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
3.7
作者：
Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P
通讯作者：
Ribeca P