Introduction
Use the strategy FREEC-SV to call Structural Variants and Copy Number Alterations from your deep-sequencing data! This means to run
FREEC (to find copy number alterations) and
SVDetect (to detect large structural variants) and combine their outputs.
Intersection of FREEC and SVDetect outputs allows one to (1) refine coordinates of CNAs using PEM data and (2)
improve confidence in calling true positive rearrangements (particularly, in ambiguous satellite/repetitive regions).
Both SVDetect and FREEC are compatible with the SAM alignment format and provide output files for graphical visualization of predicted genomic rearrangements.
About FREEC:
FREEC is a tool for control-free (or not) copy number alteration (gains and losses) detection using deep-sequencing data.
FREEC automatically computes, normalizes, segments copy number profiles and calls copy number alterations.
FREEC can use mappability data (files created by GEM).
Input: Aligned single-end, paired-end or mate-pair data in SAM, SAMtools pileup, Eland, BED, SOAP or Bowtie formats.
Output: Regions of gains and lossed, copy number profiles.
About SVDetect :
SVDetect is a tool for detection of intra- and inter-chromosomal rearrangements
from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.
Input: Aligned paired-end or mate-pair data in SAM, BAM, Eland or Bioscope formats.
Output: Table with predicted structural variants:
deletions, insertions, inversions, insertions of a known genomic fragment, large tandem duplications, inverted duplications, balanced and unbalanced translocations, co-amplicons etc.
(see SVDetect tutorial).
Both applications are developed by the
Bioinformatics Laboratory of Institut Curie (Paris).
To cite FREEC:
Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
Bioinformatics 2011; 27(2):268-9. PMID: 21081509. (PDF,
abstract).
To cite SVDetect:
Bruno Zeitouni; Valentina Boeva; Isabelle Janoueix-Lerosey; Sophie Loeillet; Patricia Legoix-ne; Alain Nicolas; Olivier Delattre; Emmanuel Barillot (2010)
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Bioinformatics 2010; 26: 1895-1896. (PDF,
abstract).
More information is available:
Downloads
- Download and install FREEC here
- Download and install SVDetect here
- Download scripts to combine the output of the two programs here
FREEC and SVDetect working group
Contacts
The following members of the FREEC working group are pleased to answer any question or address any concerns you may have with the FREEC or SVDetect software:
Acknowledgements
This work was supported by grants from the Institut National de la Sante et de la Recherche Medicale,
the Institut Curie, the Ligue Nationale contre le Cancer (Equipe labellisee and CIT program). We thank Tatiana Popova and Joern Toedling
for valuable discussion.
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