WGSA: an annotation pipeline for human genome sequencing studies.
作者信息
Liu Xiaoming, White Simon, Peng Bo, Johnson Andrew D, Brody Jennifer A, Li Alexander H, Huang Zhuoyi, Carroll Andrew, Wei Peng, Gibbs Richard, Klein Robert J, Boerwinkle Eric
机构信息
Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA.
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
出版信息
J Med Genet. 2016 Feb;53(2):111-2. doi: 10.1136/jmedgenet-2015-103423. Epub 2015 Sep 22.
Abstract
摘要
相似文献
1
WGSA: an annotation pipeline for human genome sequencing studies.
J Med Genet. 2016 Feb;53(2):111-2. doi: 10.1136/jmedgenet-2015-103423. Epub 2015 Sep 22.
2
GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.
Gene. 2013 Apr 10;518(1):114-23. doi: 10.1016/j.gene.2012.11.063. Epub 2013 Jan 12.
3
Gene calling and bacterial genome annotation with BG7.
Methods Mol Biol. 2015;1231:177-89. doi: 10.1007/978-1-4939-1720-4_12.
4
UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.
PLoS One. 2015 May 28;10(5):e0128026. doi: 10.1371/journal.pone.0128026. eCollection 2015.
5
Simple high-throughput annotation pipeline (SHAP).
Bioinformatics. 2011 Sep 1;27(17):2431-2. doi: 10.1093/bioinformatics/btr411. Epub 2011 Jul 19.
6
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.
DNA Res. 2015 Oct;22(5):319-29. doi: 10.1093/dnares/dsv015. Epub 2015 Sep 3.
7
A test drive of a DNA-analysis toolkit in the cloud.
Nature. 2017 Dec 7;552(7683):137-138. doi: 10.1038/d41586-017-07833-1.
8
MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.
FEMS Microbiol Lett. 2016 Apr;363(7). doi: 10.1093/femsle/fnw049. Epub 2016 Mar 1.
9
myMIR: a genome-wide microRNA targets identification and annotation tool.
Brief Bioinform. 2011 Nov;12(6):588-600. doi: 10.1093/bib/bbr062. Epub 2011 Oct 22.
10
GASS: genome structural annotation for Eukaryotes based on species similarity.
BMC Genomics. 2015 Mar 4;16(1):150. doi: 10.1186/s12864-015-1353-3.
引用本文的文献
1
Leveraging functional annotations to map rare variants associated with Alzheimer disease with gruyere.
Am J Hum Genet. 2025 Aug 13. doi: 10.1016/j.ajhg.2025.07.016.
2
Genomic loci and molecular genetic mechanisms for hidradenitis suppurativa.
Br J Dermatol. 2025 Jul 12. doi: 10.1093/bjd/ljaf277.
3
Region-Based Analysis with Functional Annotation Identifies Genes Associated with Cognitive Function in South Asians from India.
Genes (Basel). 2025 May 27;16(6):640. doi: 10.3390/genes16060640.
4
Cross-Ancestry Comparison of Aptamer and Antibody Proteomics Measures.
Res Sq. 2025 Feb 13:rs.3.rs-5968391. doi: 10.21203/rs.3.rs-5968391/v1.
5
Leveraging functional annotations to map rare variants associated with Alzheimer's disease with gruyere.
medRxiv. 2025 Mar 4:2024.12.06.24318577. doi: 10.1101/2024.12.06.24318577.
6
Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.
Hum Genomics. 2024 Nov 5;18(1):120. doi: 10.1186/s40246-024-00684-8.
7
Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.
Hum Genomics. 2024 Aug 28;18(1):90. doi: 10.1186/s40246-024-00663-z.
8
Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians from India.
Res Sq. 2024 Aug 10:rs.3.rs-4712660. doi: 10.21203/rs.3.rs-4712660/v1.
9
Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.
bioRxiv. 2024 Jun 28:2024.06.25.600283. doi: 10.1101/2024.06.25.600283.
10
Variants in Candidate Genes for Phenotype Heterogeneity in Patients with the 22q11.2 Deletion Syndrome.
Genet Res (Camb). 2024 Mar 30;2024:5549592. doi: 10.1155/2024/5549592. eCollection 2024.
本文引用的文献
1
Ensembl 2015.
Nucleic Acids Res. 2015 Jan;43(Database issue):D662-9. doi: 10.1093/nar/gku1010. Epub 2014 Oct 28.
2
Choice of transcripts and software has a large effect on variant annotation.
Genome Med. 2014 Mar 31;6(3):26. doi: 10.1186/gm543. eCollection 2014.
3
RefSeq: an update on mammalian reference sequences.
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. doi: 10.1093/nar/gkt1114. Epub 2013 Nov 19.
4
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.
Hum Mutat. 2013 Sep;34(9):E2393-402. doi: 10.1002/humu.22376. Epub 2013 Jul 10.
5
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 Apr-Jun;6(2):80-92. doi: 10.4161/fly.19695.
6
dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions.
Hum Mutat. 2011 Aug;32(8):894-9. doi: 10.1002/humu.21517.
7
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Nucleic Acids Res. 2010 Sep;38(16):e164. doi: 10.1093/nar/gkq603. Epub 2010 Jul 3.
8
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
Bioinformatics. 2010 Aug 15;26(16):2069-70. doi: 10.1093/bioinformatics/btq330. Epub 2010 Jun 18.
Zotero 插件