Indexcov: fast coverage quality control for whole-genome sequencing
Indexcov: fast coverage quality control for whole-genome sequencing
复制标题
DOI：
10.1093/gigascience/gix090
复制
发表时间：
2017-09-18
期刊：
影响因子：
9.2
通讯作者：
Quinlan, Aaron R.
中科院分区：
文献类型：
--
作者：
Pedersen, Brent S.;Collins, Ryan L.;Quinlan, Aaron R.
BAM和CRAM格式提供了一个补充的线性索引，方便快速访问任意基因组区域的序列比对。比较BAM或CRAM索引中的连续条目，可以推断每个基因组区域的比对记录数量，作为每个基因组区域序列深度的有效代理。基于这些特性，我们开发了indexcov，这是一种高效的全基因组测序覆盖估计器，可快速识别具有异常覆盖概况的样本，揭示大规模染色体异常，识别潜在的批次效应，并推断样本的性别。Indexcov在MIT许可下可在https://github.com/brentp/goleft获得。
The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license.