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APOLLOH specifications


Unique identifier OMICS_00306
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The set of genome-wide heterozygous SNP positions inferred from the normal genome, the copy number profiles inferred from the tumor genome, and the allelic counts of the tumor data for each heterozygous SNP position.
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Sohrab P. Shah

Publication for APOLLOH

APOLLOH citations


Detection and genomic characterization of a mammary like adenocarcinoma

PMCID: 5701302
PMID: 28877932
DOI: 10.1101/mcs.a002170

[…] tion was done with the Ensemble database (v69), and the effect calculation was assisted by annotations from SnpEff 3.2 (), COSMIC v64, and dbSNP v137. LOH events and tumor content were estimated with APOLLOH v0.1.1 (). Copy-number variants were identified using CNAseq v0.0.6 (https://www.bcgsc.ca/platform/bioinfo/software/cnaseq).RNA-seq data were analyzed using JAGuaR v2.0.3 (). The RNA-seq data […]


Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma

PMCID: 5593158
PMID: 28514723
DOI: 10.1101/mcs.a001628

[…] copy-number alterations) ratios and allelic frequencies of each chromosome (; ). The tumor and matched normal samples were analyzed in conjunction to identify LOH and CNVs with CNAseq (v0.0.6) () and APOLLOH (v0.1.1) (), respectively. The collection of distinct CNA and loss of LOH regions was compared with a set of theoretical models for ploidy (ranging from diploid to pentaploid) and tumor conten […]


Molecular etiology of an indolent lymphoproliferative disorder determined by whole genome sequencing

PMCID: 4849852
PMID: 27148583
DOI: 10.1101/mcs.a000679

[…] ltered with varFilter. The tumor sample was compared with the normal sample to identify somatic copy-number variants (CNAseq v0.0.6, http://www.bcgsc.ca/platform/bioinfo/software/cnaseq), LOH events (APOLLOH v0.1.1, using the “K18 params Illumina stromalRatio Hyper10k min10max200” parameter matrix, downloaded from http://compbio.bccrc.ca/software/apolloh/) (), single-nucleotide variants (SAMtools […]


Putative BRAF activating fusion in a medullary thyroid cancer

PMCID: 4849853
PMID: 27148585
DOI: 10.1101/mcs.a000729

[…] s compared with that of the patient's constitutive DNA to identify somatic alterations. Regions of copy-number variation and LOH were determined using hidden Markov model–based approaches HMMcopy and APOLLOH (), respectively. De novo assembly and annotation of genomic data using ABySS and Trans-ABySS () were used to identify small insertions and deletions (indels) and large structural variants (SV […]


Computational characterisation of cancer molecular profiles derived using next generation sequencing

PMCID: 4322529
PMID: 25691827
DOI: 10.5114/wo.2014.47137

[…] tification of all types of somatic mutations []. Several methods for detecting somatic mutations are currently in use, such as MuTect [], Strelka [], and VarScan 2 [] for SNV detection or BIC-Seq [], APOLLOH [], CoNIEFER [], BreakDancer [], and Meerkat [] for CNA or SV detection. Most methods for somatic mutation detection take into account only part of the possible source of errors; therefore, ru […]


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APOLLOH institution(s)
Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada; Bioinformatics Training Program, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada; Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
APOLLOH funding source(s)
Supported by the Canadian Breast Cancer Foundation, the Michael Smith Foundation for Health Research, the Natural Sciences and Engineering Research Council of Canada.

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