DNAseq toolbox
From BITS wiki
NGS analysis of gDNA features (CNV or other genome remodeling events, genomic variants, ...)
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Contents
Mapping short reads to a reference genome
Have a look to the detailed overview page about Mappers.
Mapping of short reads to a reference genome with tolerance for splicing is reported in the separate RNAseq toolbox
Calling variants from mapping results
- Samtools remains the most widely used mapping analysis toolbox
- Bcftools follows Samtools in the classiccal variant analysis.
- GATK has been developped by the Broad Institute to produce better quality results presented as the 1000 genome project.
- Varscan2 was cited as a good alternative to identify low frequency variants in eg mixed tumor samples
Calling structural variants from mapping results
- Breakdancer, a popular SV tool
- SVMerge to find structural variants called by multiple callers, including Breakdancer
CNV analysis
- HMMcopy-cli as a very valuable set of command-line applications required to generate data for HMMcopy.
- HMMcopy, a Bioconductor package to find CNV after correcting for GC content
- HTSeq ([1]), a python toolbox dedicated to NGS read counting (also part of the RNAseq_toolbox).
- RDXplorer identifies CNV from BAM-formatted mapping data
ChIP-Seq
ChIP-Seq has its own ChIPseq_toolbox
References:
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