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Protocols

KGGSeq specifications

Information


Unique identifier OMICS_02260
Name KGGSeq
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Version 0.8
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Subtool


  • ISPP

Download


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Versioning


No version available

Maintainer


  • person_outline Miaoxin Li

Publications for KGGSeq

KGGSeq citations

 (26)
call_split

CD70 Deficiency due to a Novel Mutation in a Patient with Severe Chronic EBV Infection Presenting As a Periodic Fever

2018
Front Immunol
PMCID: 5796890
PMID: 29434583
DOI: 10.3389/fimmu.2017.02015
call_split See protocol

[…] were processed using the GATK framework [version 2.8.1 ()], according to the GATK best practices recommendations (, ). Variants were classified as known or novel based on dbSNP146 and annotated using KGGSeq ().Annotations included positions in UCSC, RefGene, GENCODE and ENSEMBL transcripts, OMIM and ClinVar annotations, potential false positive signals, allele frequency in dbSNP, ESP6500, 1000 Gen […]

library_books

PDE1A polymorphism contributes to the susceptibility of nephrolithiasis

2017
BMC Genomics
PMCID: 5738135
PMID: 29262781
DOI: 10.1186/s12864-017-4247-8

[…] on variants and estimated per-individual heterozygosity (~inbreeding), pairwise relatedness, and sex-check using PLINK (Additional file : Table S1). Variants quality control was conducted by software KGGSeq (http://statgenpro.psychiatry.hku.hk/limx/kggseq/ doc/UserManual.html), which were carefully designed to filter and prioritize gene variants in exome sequencing of rare Mendelian and common com […]

call_split

Rationale and design of GENEiUS: a prospective observational study on the genetic and environmental determinants of body mass index evolution in Canadian undergraduate students

2017
BMJ Open
PMCID: 5778320
PMID: 29229660
DOI: 10.1136/bmjopen-2017-019365
call_split See protocol

[…] are. Gene-based association of SNPs with obesity trait level and change will be assessed using VEGAS2 software. Variant annotation and filtering from whole-exome sequences will be performed using the KGGSEQ framework. The association of well-established GWAS SNPs for BMI, WC, WHR and %BF, or a combination of pathogenic mutations in previously identified monogenic genes, with obesity trait level an […]

library_books

Dysfunction of Myosin Light‐Chain 4 (MYL4) Leads to Heritable Atrial Cardiomyopathy With Electrical, Contractile, and Structural Components: Evidence From Genetically‐Engineered Rats

2017
PMCID: 5721782
PMID: 29080865
DOI: 10.1161/JAHA.117.007030

[…] JA5, we performed exome sequencing in 2 patients, II‐1 and II‐3. In total, 62 960 single‐nucleotide variants and 4192 insertions/deletions (Indels) were detected after stringent quality control using KGGSeq (V0.8), and we chose the top 60 single‐nucleotide variants (listed in Table ) for validation according to their predicted pathogenic probability. It turned out that 2 missense single‐nucleotide […]

library_books

Exome Sequencing of Extended Families with Alzheimer’s Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function

2017
PMCID: 5698805
PMID: 29177109
DOI: 10.4172/2161-0460.1000355

[…] Alterations passing quality measurements were annotated with the KGGSeq and ANNOVAR programs [,]. Variants were normalized prior to annotation []. Ensembl, RefSeq, and Gencode transcripts were all annotated, and the top consequence per gene was used for prioritizat […]

library_books

Rapid Identification of Pathogenic Variants in Two Cases of Charcot Marie Tooth Disease by Gene Panel Sequencing

2017
Int J Mol Sci
PMCID: 5412354
PMID: 28379183
DOI: 10.3390/ijms18040770

[…] within the exome regions included by wANNOVAR and those with allele frequency ≥0.05 in 1000 Genome project or ExAC database []. Pathogenicity prediction of nonsynonymous variants was performed using KGGSeq with default quality control criteria (--gty-qual 20 --gty-dp 4), additional option to predict Mendelian disease-causing and complex disease-causing variants (--mendel-causing-predict best --db […]

Citations

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KGGSeq institution(s)
Department of Psychiatry; State Key Laboratory for Cognitive and Brain Sciences; Centre for Reproduction, Development and Growth; Genome Research Centre; Department of Medicine; Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong, China

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