News
[11/17/2016]
Scalpel protocol now published in Nature Protocols:
Fang H., Bergmann E.A., Arora K., Vacic V., Zody M.C., Iossifov I., O'Rawe J.A., Wu Y., Jimenez Barron L.T., Rosenbaum J., Ronemus M., Lee Y., Wang Z., Dikoglu E., Jobanputra V., Lyon G.J., Wigler M., Schatz M.C., Narzisi G.
Indel variant analysis of short-read sequencing data with Scalpel.
Nature Protocols 11, 2529–2548, 2016. (DOI: 10.1038/nprot.2016.150)
[11/11/2016]
A docker image of scalpel is available here: scalpel docker image
[10/05/2015]
Scalpel (v0.5.2) available for download at SourceForge.
Fixed critical bug (in two-pass mode) causing calls with low support in the normal to be exported as somatic. Updating is highly recommended!
[10/1/2015]
Preprint of "Indel variant analysis of short-read sequencing data with Scalpel" published on the bioRxiv:
Fang H., Grabowska E.A., Arora K., Vacic V., Zody M.C., Iossifov I., ORawe J.A, Wu Y, Jimenez Barron L.T, Rosenbaum J., Ronemus M., Lee Y., Wang Z., Lyon G.J, Wigler M., Schatz M.C., Narzisi G.
Indel variant analysis of short-read sequencing data with Scalpel
bioRxiv (DOI: 10.1101/028050)
[09/21/2015]
Scalpel version 0.5.1 (beta) is now available for download at
SourceForge.
Changes include a new command-line user interface, better scoring of somatic variants, and enhanced functionalities for the export tool.
[04/19/2015]
Scalpel version 0.4.1 (beta) is now available for download at
SourceForge.
Changes include modification of the core algorithms for higher sensitivity and various code optimizations to improve speed.
[11/11/2014]
Scalpel version 0.3.1 (beta) is now available for download at SourceForge.
[10/28/2014]
New paper published highlighting the use of Scalpel to reduce errors in whole-genome and whole-exome studies:
Fang H., Narzisi G., O'Rawe J., Wu Y., Rosenbaum J., Ronemus M., Iossifov I., Schatz M.C., Lyon G.J.
Reducing INDEL calling errors in whole-genome and exome sequencing data.
Genome Medicine 2014, 6:89 (DOI: 10.1186/s13073-014-0089-z).
Also available at the CSHL bioRxiv 2014 (DOI: 10.1101/006148).
[08/17/2014]
Scalpel manuscript published in Nature Methods
(DOI: 10.1038/nmeth.3069).
[Press Release (CSHL)]
[Press Release (SFARI)]
[08/15/2014]
Scalpel version 0.2.1 (beta) is now available for download at SourceForge.
[12/11/2013]
The first public (0.1.1 beta) release of Scalpel is now available for download at SourceForge.
[12/13/2013]
Preprint of the Scalpel paper published on the bioRxiv:
Narzisi G., O'Rawe J.A., Iossifov I., Fang. H., Lee Y., Wang Z., Wu Y., Lyon G.J., Wigler M., Schatz M.C.
Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly
bioRxiv (DOI: 10.1101/001370)