Scalpel: Indel 变异鉴定工具,支持单样本、家庭样本以及正常和肿瘤对样本


Indel variant analysis of short-read sequencing data with Scalpel.


As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel ( is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequencing data. We provide detailed instructions for an exemplary family-based de novo study, but we also characterize the other two supported modes of operation: single-sample and somatic analysis. Indel normalization, visualization and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ~5 h after read mapping.




tar xzvf  scalpel-0.5.3.tar.gz
cd scalpel-0.5.3


Nature Protocols 杂志发表了不少优秀生物信息工具Protocol,比如:Trinity RNA-seq 拼装如软件平台,HISAT,StringTie and Ballgown RNA-seq 分析套件, 这次导读的是Nature Protocols上刚出版的 INDEL鉴定工具 Scalpel

在执行 INDEL 鉴定之前基本可以按照 Broad GATK 最佳实践 或者 Speedseq 最佳实践执行预处理, 其中GATK最佳实践: BWA-MEM + SAMTOOLS + PICARD , Speedseq 最佳实践: BWA-MEM + Sambamba + SAMBLASTER , 通常我们鉴定 INDEL 可能直接 GATK 或者 FreeBayes

Scalpel 除了可以处理单样本indels鉴定, 也提供了家庭装,鉴定Inherited indelsDe novo indels, 同时也可以鉴定正常样本和肿瘤样本的 Somatic indels,可作为GATK或者FreeBayes 流程之外的扩展。

Scalpel protocol 主要步骤

Scalpel protocol



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