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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


No version available


  • person_outline Gavin Ha

Publication for HMMcopy

HMMcopy citations


Whole exome sequencing of cell free DNA and circulating tumor cells in multiple myeloma

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

[…] of 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 […]


Genomic profiling of dedifferentiated liposarcoma compared to matched well differentiated liposarcoma reveals higher genomic complexity and a common origin

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

[…] matched 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 alterat […]


Single nucleotide variant profiles of viable single circulating tumour cells reveal CTC behaviours in breast cancer

PMCID: 5928770
PMID: 29565466
DOI: 10.3892/or.2018.6325
call_split See protocol

[…] ngle 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. […]


Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

Sci Rep
PMCID: 5717219
PMID: 29208983
DOI: 10.1038/s41598-017-16813-4
call_split See protocol

[…] higher 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. […]


Single cell multi omics sequencing of mouse early embryos and embryonic stem cells

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

[…] ndividual ES cells and used readCounter to bin the genome into consecutive 100 kb tiles, then calculated the absolute number of reads detected in each window. After correction and normalization using HMMcopy, we calculated the averaged read counts of 100 kb tiles that overlapped with DNA replication domains in each single ES cell. The mean values of counts in the leading and lagging replication re […]


Pancreatic cancer ascites xenograft–an expeditious model mirroring advanced therapeutic resistant disease

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

[…] enograft 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. […]


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

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