FishingCNV statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

FishingCNV specifications

Information


Unique identifier OMICS_00334
Name FishingCNV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for FishingCNV

FishingCNV citations

 (9)
call_split

Characterizing temporal genomic heterogeneity in pediatric high grade gliomas

2017
PMCID: 5663045
PMID: 29084603
DOI: 10.1186/s40478-017-0479-8
call_split See protocol

[…] s using an in-house program (CNAXX; unpublished) we developed that takes both coverage (normalized average) and the deviation of B allele frequency from 50% into account (adapted from methods used in FishingCNV [] and ExomeAI []). Different CNV events (amplification, deletion and copy neutral LOH) were called based upon the status of the normalized coverage and the B allelic imbalance as we descri […]

call_split

Development and clinical utility of a novel diagnostic nystagmus gene panel using targeted next generation sequencing

2017
Eur J Hum Genet
PMCID: 5477371
PMID: 28378818
DOI: 10.1038/ejhg.2017.44
call_split See protocol

[…] cal realignment around indels and recalibrate quality scores. Single-nucleotide variants and indels were detected using GATK. Further annotation and filtering was performed using ANNOVAR. We utilised FishingCNV v2.1 for copy number variation analyses.We determined the assay sensitivity, specificity and balanced accuracy for the NA12878 sample by computing the true positives (TP), false positives ( […]

library_books

Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma

2016
Nat Commun
PMCID: 4823825
PMID: 27048880
DOI: 10.1038/ncomms11185

[…] in our samples we developed an in-house program to calculate the deviation of B allele frequency from 50% as well as normalized coverage from whole exome sequencing data (adapted from methods used in FishingCNV and ExomeAI). Different CNV events (duplication, deletion and copy neutral LOH) were called based upon the B allelic imbalance and the status of the normalized coverage as follow: deviation […]

library_books

Enhanced diagnostic yield in Meckel Gruber and Joubert syndrome through exome sequencing supplemented with split read mapping

2016
BMC Med Genet
PMCID: 4700600
PMID: 26729329
DOI: 10.1186/s12881-015-0265-z

[…] targeted genomic intervals was calculated for each patient using the GATK DepthOfCoverage walker. Exon-based copy number analysis was performed on coordinate-sorted duplicate-cleaned BAM files using FishingCNV v.2.1 []. The reference control pool for the copy number analyses comprised 65 patients referred for disorders other than JBTS or MKS. Inter-batch variability was reduced using the FishingC […]

library_books

A distinctive oral phenotype points to FAM20A mutations not identified by Sanger sequencing

2015
PMCID: 4694127
PMID: 26740946
DOI: 10.1002/mgg3.164

[…] this result, whole exome sequencing was performed on a second aliquot of DNA from the same individual. The resulting data were aligned to the human hg19 genome and dosage analysis was performed using FishingCNV by comparing this sample to a cohort of 50 non‐AI‐affected controls. Exomes from all controls and the AI‐affected sample had been captured, sequenced and analyzed using consistent methodolo […]

library_books

Rapid Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD): exome sequencing of trios, monozygotic twins and tumours

2015
Orphanet J Rare Dis
PMCID: 4548308
PMID: 26302956
DOI: 10.1186/s13023-015-0314-x

[…] al translocation and inter-chromosomal insertions located inside exons in all 16 ROHHAD proband exomes (the 7 discovery cohort trio probands and the 9 replication cohort exomes) and 4 tumour samples. FishingCNV v2.1 [] was used to search for genomic copy number variants (CNVs) in the seven trio ROHHAD probands within the discovery cohort. Exomes from 22 healthy individuals, sequenced with the same […]

Citations

Looking to check out a full list of citations?

FishingCNV institution(s)
Department of Human Genetics, McGill University, Montreal, QC, Canada

FishingCNV reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FishingCNV