FishingCNV statistics

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Protocols

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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

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Publication for FishingCNV

FishingCNV in pipeline

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

[…] protocol. raw sequence reads for a pool of six exome libraries were demultiplexed and aligned to hg19 using bwa v0.6.2. picard v1.85 removed duplicate reads. dosage analysis was performed using fishingcnv (shi and majewski ) by comparing this sample to a cohort of 50 non‐ai‐affected controls., the proband of family 1 is a 17‐year‐old male born of unrelated parents of different ethnic […]


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FishingCNV in publications

 (7)
PMCID: 5663045
PMID: 29084603
DOI: 10.1186/s40478-017-0479-8

[…] using an in-house program (cnaxx; unpublished) we developed that takes both coverage (normalized average) and the deviation of b allele frequency from 50% into account (adapted from methods used in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 […]

PMCID: 5477371
PMID: 28378818
DOI: 10.1038/ejhg.2017.44

[…] 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 […]

PMCID: 4823825
PMID: 27048880
DOI: 10.1038/ncomms11185

[…] 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: […]

PMCID: 4700600
PMID: 26729329
DOI: 10.1186/s12881-015-0265-z

[…] cases (4 %). seeking to determine whether our cohort harboured pathogenic copy number variants (cnv), in jbts- or mks-associated genes, targeted comparative read-depth analysis was performed using fishingcnv. these analyses identified a putative intragenic ahi1 deletion that included three exons spanning at least 3.4 kb and an intergenic mpp4 to tmem237 deletion that included exons spanning […]

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

[…] protocol. raw sequence reads for a pool of six exome libraries were demultiplexed and aligned to hg19 using bwa v0.6.2. picard v1.85 removed duplicate reads. dosage analysis was performed using fishingcnv (shi and majewski ) by comparing this sample to a cohort of 50 non‐ai‐affected controls., the proband of family 1 is a 17‐year‐old male born of unrelated parents of different ethnic […]


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

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