APOLLOH 0.1.1 – HMM for Profiling Loss of Heterozygosity in Whole Cancer Genome Shotgun Sequencing data

APOLLOH 0.1.1

:: DESCRIPTION

APOLLOH is a hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Matlab

:: DOWNLOAD

APOLLOH

:: MORE INFORMATION

Citation

G. Ha, A. Roth, D. Lai, A. Bashashati, J. Ding, R. Goya, R. Giuliany, J. Rosner, A. Oloumi, K. Shumansky, S.-F. Chin, G. Turashvili, M. Hirst, C. Caldas, M. A. Marra, S. Aparicio, S. P. Shah.
Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer.
Genome Research 2012, 2012 Oct;22(10):1995-2007.

CLImAT 1.2.2 – Detection of Copy Number Alteration and Loss of Heterozygosity

CLImAT 1.2.2

:: DESCRIPTION

CLImAT (CNA and LOH Assessment in Impure and Aneuploid Tumors) is a bioinformatic tool for identification of genome-wide aberrations from tumor samples using whole-genome sequencing data.

::DEVELOPER

HI_Lab @ USTC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
Matlab

:: DOWNLOAD

CLImAT

:: MORE INFORMATION

Citation:

CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data.
Yu Z, Liu Y, Shen Y, Wang M, Li A.
Bioinformatics. 2014 Sep 15;30(18):2576-83. doi: 10.1093/bioinformatics/btu346.

ROHan v1.0 – Joint inference of Runs of Homozygosity and rates of Heterozygosity

ROHan v1.0

:: DESCRIPTION

ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity outside of ROHs. ROHan can work on modern and ancient samples with signs of ancient DNA damage.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ROHan

:: MORE INFORMATION

Citation

Renaud G, Hanghoj K, Korneliussen TS, Willerslev E, Orlando L.
Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.
Genetics. 2019 Jul;212(3):587-614. doi: 10.1534/genetics.119.302057. Epub 2019 May 14. PMID: 31088861; PMCID: PMC6614887.

hapLOH 14 – Analysis of loss of Heterozygosity in Tumor Genomes

hapLOH 1.4

:: DESCRIPTION

hapLOH profiles and characterizes tumor genomes using data from SNP microarrays. It is designed to be effective in the presence of high levels of germline contamination.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
Perl
Python

:: DOWNLOAD

hapLOH

:: MORE INFORMATION

Citation

Vattathil, Selina, and Paul Scheet.
“Haplotype-based profiling of subtle allelic imbalance with SNP arrays.”
Genome research 23.1 (2013): 152-158.

ExomeCNV 1.4 – Exome Sequencing-based Copy-number Variation and Loss of Heterozygosity Detection

ExomeCNV 1.4

:: DESCRIPTION

ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads.

::DEVELOPER

Nelsonlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R package
Perl
Python
Samtool
GATK

:: DOWNLOAD

ExomeCNV

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF.