ASCAT pipeline

ASCAT specifications

Information


Unique identifier OMICS_02570
Name ASCAT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.5.1
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Vessela Kristensen <>

Publication for ASCAT

ASCAT citation

2014
PMCID: 4029584

[…] provide accurate information of the primary tumor cells, which are heterogeneous with mixtures of normal and cancerous cells. to solve this issue, the allele-specific copy number analysis of tumors (ascat) [24] provides whole-genome allele-specific copy number and construct a genome-wide map of loci with alleles that were preferentially lost, pointing to candidate genes that may drive cancer […]

ASCAT institution(s)
Department of Genetics, Institute for Cancer Research, Clinic for Cancer and Surgery, Oslo University Hospital, Oslo, Norway; Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium; Department of Human Genetics, University of Leuven, Leuven, Belgium; Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA; Department of Informatics, University of Oslo, Blindern, Oslo, Norway; Department of Pathology, Clinic for Cancer and Surgery, Oslo University Hospital, Oslo, Norway; Institute for Clinical Medicine, University of Oslo, Oslo, Norway; Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA; Department of Oncology-Pathology, Karolinska Institute, Cancer Center Karolinska, Stockholm, Sweden; The Cancer Clinic, Clinic for Cancer and Surgery, Oslo University Hospital, Montebello, Oslo, Norway; Institute for Clinical Epidemiology and Molecular Biology, Akershus University Hospital, Faculty of Medicine, University of Oslo, Nordbyhagen, Norway
ASCAT funding source(s)
Supported by Norwegian Research Council Grants 155218/V40 and 175240/S10, Functional Genomics-Norsk Forskningsråd (Norwegian Research Council) (FUGE-NFR) FUGE-NFR 181600/V11, and a Swizz Bridge Award and by Norwegian Cancer Society Grants D99061 and D03067, by the Research Foundation-Flanders (FWO), by travel grants from the FWO and from the European Association for Cancer Research, doctoral fellow of the Norwegian Cancer Association (PK01-2007-0356), by a travel grant from Lillemor Grobstoks Legacy for Cancer Research, by National Cancer Institute Breast Specialized Program of Research Excellence Grant P50-CA58223-09A1, the Breast Cancer Research Foundation, and the V Foundation for Cancer Research.

ASCAT reviews

 (2)
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Fabien Pichon

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For CNV identification. Works well. The paper is very clear, very well explained ! A lot of usefull plots. Sometimes, it cannot resolve the couple (ploidy, aberrent fraction cell) shown in the sunrise plot. I thus used Noise-free-CNV-filter to normalize data before ASCAT, but it didn't help to resolve these samples. Hopefully, Peter van Loo has added the possibility to manually define it in the new version.
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Mmoisse

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I'm very happy with this tool to find SCNA in cancer genomes without the need of a matched normal.
To remove CG-noise in the data I use PennCNV prior to ASCAT, it works very well in most of the samples.