APOLLOH protocols

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APOLLOH specifications

Information


Unique identifier OMICS_00306
Name APOLLOH
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

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Maintainer


  • person_outline Sohrab P. Shah <>

Publication for APOLLOH

APOLLOH in pipeline

2016
PMCID: 4849853
PMID: 27148585
DOI: 10.1101/mcs.a000729

[…] 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 […]


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APOLLOH in publications

 (7)
PMCID: 5793777
PMID: 29092957
DOI: 10.1101/mcs.a002329

[…] variants (snvs) and small insertions/deletions were processed using samtools () and strelka (v0.4.6.2) (). regions of copy-number aberration (cna) were determined using cnaseq (v0.0.6) and loh by apolloh (v0.1.1) (). tumor content and ploidy models were estimated from sequencing data through analysis of the cna ratios and allelic frequencies of each chromosome. this was then compared […]

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

[…] 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)., na, not available; pcr, polymerase chain reaction; ssrna, […]

PMCID: 5312317
PMID: 27449082
DOI: 10.18632/oncotarget.10661

[…] and tumor were then aligned to the human reference genome build grch37 using bwa (v0.5.7). data from multiple lanes were merged and duplicates identified using picard (v1.38). cnaseq (v0.0.6) and apolloh (v0.1.1) were used to identify copy number aberrations and loss of heterozygosity respectively. for identification of single nucleotide variants, samtools (v1.0.2) was applied followed […]

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

[…] 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 […]

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

[…] 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 […]


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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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