LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files

Abstract The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed...

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Vydáno v:	Briefings in bioinformatics Ročník 22; číslo 4
Hlavní autoři:	Dong, Shan-Shan, He, Wei-Ming, Ji, Jing-Jing, Zhang, Chi, Guo, Yan, Yang, Tie-Lin
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Oxford Oxford University Press 01.07.2021 Oxford Publishing Limited (England)
Témata:	Annotations Format Haplotypes Linkage disequilibrium Population genetics Population studies Single-nucleotide polymorphism Subgroups visualization VCF files haplotype block linkage disequilibrium
ISSN:	1467-5463, 1477-4054, 1477-4054
On-line přístup:	Získat plný text
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Abstract	Abstract The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03–13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists.
AbstractList	Abstract The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03–13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists. The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03–13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists. The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03-13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists.The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03-13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists. The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03–13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists.
Author	Ji, Jing-Jing Zhang, Chi Guo, Yan Yang, Tie-Lin He, Wei-Ming Dong, Shan-Shan
Author_xml	– sequence: 1 givenname: Shan-Shan surname: Dong fullname: Dong, Shan-Shan email: dongss@xjtu.edu.cn – sequence: 2 givenname: Wei-Ming orcidid: 0000-0003-0483-5390 surname: He fullname: He, Wei-Ming email: hewm@genomics.cn – sequence: 3 givenname: Jing-Jing surname: Ji fullname: Ji, Jing-Jing email: jijingjing@genomics.cn – sequence: 4 givenname: Chi surname: Zhang fullname: Zhang, Chi email: zhangchi2@bgi.com – sequence: 5 givenname: Yan surname: Guo fullname: Guo, Yan email: guoyan253@xjtu.edu.cn – sequence: 6 givenname: Tie-Lin orcidid: 0000-0001-7062-3025 surname: Yang fullname: Yang, Tie-Lin email: yangtielin@xjtu.edu.cn
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ContentType	Journal Article
Copyright	The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2020 The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Keywords	visualization VCF files haplotype block linkage disequilibrium
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PublicationTitle	Briefings in bioinformatics
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References	Chen (2021072112100887800_ref6) 2020 Chen (2021072112100887800_ref7) 2018; 102 Hill (2021072112100887800_ref11) 1968; 38 Lewontin (2021072112100887800_ref10) 1964; 49 Danecek (2021072112100887800_ref8) 2011; 27 Kim (2021072112100887800_ref4) 2019; 35 Kawabata (2021072112100887800_ref5) 2019 Kim (2021072112100887800_ref1) 2019; 10 Barrett (2021072112100887800_ref2) 2005; 21 Shin (2021072112100887800_ref3) 2006 Chang (2021072112100887800_ref9) 2015; 4 Gabriel (2021072112100887800_ref12) 2002; 296 Karczewski (2021072112100887800_ref13) 2020; 581
References_xml	– volume: 35 start-page: 4419 year: 2019 ident: 2021072112100887800_ref4 article-title: Gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz308 – volume: 10 start-page: 1852 year: 2019 ident: 2021072112100887800_ref1 article-title: Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird publication-title: Nat Commun doi: 10.1038/s41467-019-09806-6 – volume: 27 start-page: 2156 year: 2011 ident: 2021072112100887800_ref8 article-title: The variant call format and VCFtools publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr330 – volume: 102 start-page: 776 year: 2018 ident: 2021072112100887800_ref7 article-title: An osteoporosis risk SNP at 1p36.12 acts as an allele-specific enhancer to modulate LINC00339 expression via long-range loop formation publication-title: Am J Hum Genet doi: 10.1016/j.ajhg.2018.03.001 – start-page: 525 volume-title: Nat Genet year: 2020 ident: 2021072112100887800_ref6 article-title: Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement – start-page: 9 year: 2006 ident: 2021072112100887800_ref3 article-title: LDheatmap: an R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms – volume: 38 start-page: 226 year: 1968 ident: 2021072112100887800_ref11 article-title: Linkage disequilibrium in finite populations publication-title: Theor Appl Genet doi: 10.1007/BF01245622 – volume: 21 start-page: 263 year: 2005 ident: 2021072112100887800_ref2 article-title: Haploview: analysis and visualization of LD and haplotype maps publication-title: Bioinformatics doi: 10.1093/bioinformatics/bth457 – start-page: 665 volume-title: Diabetes year: 2019 ident: 2021072112100887800_ref5 article-title: Genome-wide association study confirming a strong effect of HLA and identifying variants in CSAD/lnc-ITGB7-1 on chromosome 12q13.13 associated with susceptibility to fulminant type 1 diabetes – volume: 49 start-page: 49 year: 1964 ident: 2021072112100887800_ref10 article-title: The interaction of selection and linkage. I. General considerations; heterotic models publication-title: Genetics doi: 10.1093/genetics/49.1.49 – volume: 296 start-page: 2225 year: 2002 ident: 2021072112100887800_ref12 article-title: The structure of haplotype blocks in the human genome publication-title: Science doi: 10.1126/science.1069424 – volume: 4 start-page: 7 year: 2015 ident: 2021072112100887800_ref9 article-title: Second-generation PLINK: rising to the challenge of larger and richer datasets publication-title: Gigascience doi: 10.1186/s13742-015-0047-8 – volume: 581 start-page: 434 year: 2020 ident: 2021072112100887800_ref13 article-title: The mutational constraint spectrum quantified from variation in 141,456 humans publication-title: Nature doi: 10.1038/s41586-020-2308-7
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Snippet	Abstract The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous... The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of...
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SubjectTerms	Annotations Format Haplotypes Linkage disequilibrium Population genetics Population studies Single-nucleotide polymorphism Subgroups
Title	LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files
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