WGSA: An annotation pipeline for human genome sequencing studies

Journal of Medical Genetics

Volumn 53, Issue 2, 2015, Pages 111-112

  Liu, Xiaoming ^a   White, Simon ^b   Peng, Bo ^c   Johnson, Andrew D ^d,e   Brody, Jennifer A ^f   Li, Alexander H ^a   Huang, Zhuoyi ^b   Carroll, Andrew ^g   Wei, Peng ^a   Gibbs, Richard ^b   Klein, Robert J ^h   Boerwinkle, Eric ^a,b  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF TEXAS   (United States)

^d FRAMINGHAM HEART STUDY   (United States)

^e NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^f UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^g DNAnexus   (United States)

^h MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; DATA BASE; DNA SEQUENCE; EPIGENETICS; GENE FREQUENCY; GENETIC ASSOCIATION; GENOME ANALYSIS; HUMAN; INDEL MUTATION; PREDICTION; PRIORITY JOURNAL; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; CLOUD COMPUTING; HUMAN GENOME; MOLECULAR GENETICS; PROCEDURES; SOFTWARE;

CLOUD COMPUTING; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84958872393     PISSN: 00222593     EISSN: 14686244     Source Type: Journal    
DOI: 10.1136/jmedgenet-2015-103423     Document Type: Article

References (8)

1. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010;38:e164.
2. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012;6:80-92.
3. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010;26:2069-70.
4. Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 2014;42:D756-63.
5. Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SMJ, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P. Ensembl 2015. Nucleic Acids Res 2015;43:D662-9.
6. McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, The WGS500 Consortium, Cazier J-B, Donnelly P. Choice of transcripts and software has a large effect on variant annotation. Genome Med 2014;6:26.
7. Liu X, Jian X, Boerwinkle E. dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 2011;32:894-9.
8. Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat 2013;34: E2393-402.