DNAseq toolbox

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NGS analysis of gDNA features (CNV or other genome remodeling events, genomic variants, ...)

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Mapping short reads to a reference genome

Have a look to the detailed overview page about Mappers.

  • bwa the Burrows-Wheeler transform Aligner
  • maq, the older standard

Technical.png 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

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


Handicon.png ChIP-Seq has its own ChIPseq_toolbox

  1. http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html#tour

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