Tag: CNVs

CNVstat 1.0 – Statistical Association Analysis of Copy Number Variants (CNVs)

CNVstat 1.0

:: DESCRIPTION

CNVstat is a command-line program written in C for the statistical association analysis of CNVs and SNPs. CNVstat allows the user to estimate or test the effects of CNVs and SNPs by maximizing the (observed-data) likelihood that properly accounts for differential measurement errors and calling uncertainties.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 CNVstat

:: MORE INFORMATION

Citation

Hu, Y. J., Lin, D. Y. Sun, W., and Zeng, D.
“A Likelihood-Based Framework for Association Analysis of Allele-Specific Copy Numbers”.
Submitted for publication.

sciCNV – Inferring CNVs from scRNA-seq

sciCNV

:: DESCRIPTION

sciCNV dissects the effects of DNA copy number variations on transcriptional programs at single-cell resolution

::DEVELOPER

Tiedemann Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

sciCNV

:: MORE INFORMATION

Citation

Mahdipour-Shirayeh A, Erdmann N, Leung-Hagesteijn C, Tiedemann RE.
ciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution.
Brief Bioinform. 2021 Oct 15:bbab413. doi: 10.1093/bib/bbab413. Epub ahead of print. PMID: 34655292.

MATCHCLIPS 2 – Identifying the Breakpoints and CNVs

MATCHCLIPS 2

:: DESCRIPTION

MATCHCLIP is a program for identifying the breakpoints and CNVs based on the next generation sequence data using CIGAR strings.

::DEVELOPER

Hongzhe Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MATCHCLIP

:: MORE INFORMATION

Citation

Front Genet. 2013 Aug 16;4:157. doi: 10.3389/fgene.2013.00157. eCollection 2013.
MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads.
Wu Y1, Tian L, Pirastu M, Stambolian D, Li H.

ERDS 1.1 – Calling CNVs from Whole Genome NGS data

ERDS 1.1

:: DESCRIPTION

ERDS (estimation by read depth with single-nucleotide variants) is designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data, utilizing information from read depth of short reads and SNV heterozygosity.

::DEVELOPER

Mingfu Zhu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ERDS

:: MORE INFORMATION

Citation

Am J Hum Genet. 2012 Sep 7;91(3):408-21. doi: 10.1016/j.ajhg.2012.07.004. Epub 2012 Aug 30.
Using ERDS to infer copy-number variants in high-coverage genomes.
Zhu M1, Need AC, Han Y, Ge D, Maia JM, Zhu Q, Heinzen EL, Cirulli ET, Pelak K, He M, Ruzzo EK, Gumbs C, Singh A, Feng S, Shianna KV, Goldstein DB.

CANOES 0.1 – Detecting CNVs from Exome Sequencing data

CANOES 0.1

:: DESCRIPTION

CANOES is a new method to call CNVs from exome sequencing data with arbitrary number of reference samples.

::DEVELOPER

Shen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • R

:: DOWNLOAD

  CANOES

:: MORE INFORMATION

Citation

Backenroth D, Homsy J, Murillo LR, Glessner J, Lin E, Brueckner M, Lifton R, Goldmuntz E, Chung WK, Shen Y.
CANOES: detecting rare copy number variants from whole exome sequencing data.
Nucleic Acids Res. 2014 Jul;42(12):e97. doi: 10.1093/nar/gku345. Epub 2014 Apr 25. PMID: 24771342; PMCID: PMC4081054.

Zinfandel v0.9 – Detecting CNVs from Low-pass WGS data

Zinfandel v0.9

:: DESCRIPTION

Zinfandel is a tool for detecting CNVs from low-pass WGS data.

::DEVELOPER

Shen Lab & Itsik Pe’er Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Zinfandel

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011;12 Suppl 6:S4. doi: 10.1186/1471-2105-12-S6-S4.
A hidden Markov model for copy number variant prediction from whole genome resequencing data.
Shen Y, Gu Y, Pe’er I.

cnvOffSeq 0.1.2 – Detecting & Genotyping intergenic CNVs using off-target Exome data

cnvOffSeq 0.1.2

:: DESCRIPTION

cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.

::DEVELOPER

cnvOffSeq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux /Windows
  • Java

:: DOWNLOAD

 cnvOffSeq

:: MORE INFORMATION

Citation:

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.
Bellos E, Coin LJ.
Bioinformatics. 2014 Sep 1;30(17):i639-i645.

GENSENG 0.4 – Detecting CNVs from NGS data

GENSENG 0.4

:: DESCRIPTION

GENSENG is a software detecting CNVs(Copy Number Variations) from NGS(Next Generation Sequencing) data.

::DEVELOPER

Wei Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  GENSENG

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Feb 1;41(3):1519-32. doi: 10.1093/nar/gks1363. Epub 2012 Dec 28.
Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.
Szatkiewicz JP1, Wang W, Sullivan PF, Wang W, Sun W.

SegSeq 1.01 – Detect CNVs from Short Sequence Reads

SegSeq 1.01

:: DESCRIPTION

SegSeq is an algorithm to identify chromosomal breakpoints using massively parallel sequence data

::DEVELOPER

the Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SegSeq

:: MORE INFORMATION

Citation:

Nat Methods. 2009 Jan;6(1):99-103. Epub 2008 Nov 30.
High-resolution mapping of copy-number alterations with massively parallel sequencing.
Chiang DY, Getz G, Jaffe DB, O’Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES.