HMMcopy protocols

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HMMcopy specifications


Unique identifier OMICS_03363
Name HMMcopy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Gavin Ha <>

Publication for HMMcopy

HMMcopy in pipelines

PMCID: 5522335
PMID: 28489577
DOI: 10.18632/oncotarget.17253

[…] and matched normal genomes. the output of each tool was filtered to remove false positives and the resulting lists of variants were merged. somatic copy number variants (cnvs) were called by hmmcopy v0.1.1., we would like to thank dr. faiyaz notta for his valuable comments. we acknowledge the technical contributions of the production sequencing and genome sequencing informatics teams […]

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

[…] sequence was 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 […]

PMCID: 4974788
PMID: 27495311
DOI: 10.1186/s12864-016-2876-y

[…] rna-seq data are deposited at ncbi under the bioproject accession number prjna304627., dna sequencing reads were down-sampled to ~2 m reads for both k. pastoris and wildtype k. phaffii wt samples; hmmcopy (version 0.1.1) was used to evaluate the copy number in 1000 bp windows. mappability and gc content tracks were generated as control following the hmmcopy documentation. bwa (version 0.7.10) […]

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HMMcopy in publications

PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] tumor in ulp-wgs, using ichorcna,,. briefly, the genome was divided into t non-overlapping windows, or bins, of 1 mb. aligned reads were counted based on overlap within each bin using the tools in hmmcopy suite ( the read counts were then normalized to correct for gc content and mappability biases, and then cnas and tumor fraction were estimated using […]

PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] normals were obtained by first deriving segments using circular binary segmentation (cbs) () and then deriving log2 ratio scores with an in-house tool, exomecn, which is a modified version of hmmcopy () tuned for our data. for assessing amplifications and deletions, log2 scores > 0.5 were considered gains, whereas log2 scores < −0.5 were considered losses. focal somatic copy-number […]

PMCID: 5928770
PMID: 29565466
DOI: 10.3892/or.2018.6325

[…] cell., to determine the copy number, we used ginkgo (, an open-source web platform that specifically analyses single-cell copy number variants (cnvs), and two r packages (hmmcopy and dnacopy), with hg19 as the reference genome., slightly different from the ohsv1-htert-gfp-coupled facs method, the infected cells were stained with cd45 monoclonal antibody (hi30)-efluor […]

PMCID: 5717219
PMID: 29208983
DOI: 10.1038/s41598-017-16813-4

[…] gc content and mappability. the bias cannot fully be adjusted by normalizing with another next generation sequencing library (e.g. from a normal biopsy) from the same patient. we therefore use hmmcopy to adjust gc content and mappability in the read counts., unlike previous methods such as phylowgs, spruce and canopy, which capture cna or snv events as the entities in the model, our model […]

PMCID: 5539349
PMID: 28621329
DOI: 10.1038/cr.2017.82

[…] at least five wcg sites. and the pcamethods package in r was used to analyze the data., single-cell cnv analysis for cnv deduction with single-cell cool-seq data, we used the published r package hmmcopy. briefly, we used readcounter to bin the genome into consecutive 1 mb windows and calculated the absolute number of reads detected in each window. then, we used hmmcopy to estimate the copy […]

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HMMcopy institution(s)
Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada

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