VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern

Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern fr...
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Autor*in:	Hu, Qiang [verfasserIn] Wang, Dan Yan, Li Zhao, Hua Liu, Song

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2012

Schlagwörter:	Frequency Pattern Variant Call Sequence Call Variant Call Format Variant Call Format File

Anmerkung:	© Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (

Übergeordnetes Werk:	Enthalten in: BMC Research Notes - London, 2008, 5(2012), 1 vom: 14. Jan.
Übergeordnetes Werk:	volume:5 ; year:2012 ; number:1 ; day:14 ; month:01

Links:	Volltext

DOI / URN:	10.1186/1756-0500-5-31

Katalog-ID:	SPR030280117

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520			\|a Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org.
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allfields	10.1186/1756-0500-5-31 doi (DE-627)SPR030280117 (SPR)1756-0500-5-31-e DE-627 ger DE-627 rakwb eng Hu, Qiang verfasserin aut VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. Frequency Pattern (dpeaa)DE-He213 Variant Call (dpeaa)DE-He213 Sequence Call (dpeaa)DE-He213 Variant Call Format (dpeaa)DE-He213 Variant Call Format File (dpeaa)DE-He213 Wang, Dan aut Yan, Li aut Zhao, Hua aut Liu, Song aut Enthalten in BMC Research Notes London, 2008 5(2012), 1 vom: 14. Jan. (DE-627)559431805 (DE-600)2413336-X 1756-0500 nnns volume:5 year:2012 number:1 day:14 month:01 https://dx.doi.org/10.1186/1756-0500-5-31 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2012 1 14 01
spelling	10.1186/1756-0500-5-31 doi (DE-627)SPR030280117 (SPR)1756-0500-5-31-e DE-627 ger DE-627 rakwb eng Hu, Qiang verfasserin aut VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. Frequency Pattern (dpeaa)DE-He213 Variant Call (dpeaa)DE-He213 Sequence Call (dpeaa)DE-He213 Variant Call Format (dpeaa)DE-He213 Variant Call Format File (dpeaa)DE-He213 Wang, Dan aut Yan, Li aut Zhao, Hua aut Liu, Song aut Enthalten in BMC Research Notes London, 2008 5(2012), 1 vom: 14. Jan. (DE-627)559431805 (DE-600)2413336-X 1756-0500 nnns volume:5 year:2012 number:1 day:14 month:01 https://dx.doi.org/10.1186/1756-0500-5-31 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2012 1 14 01
allfields_unstemmed	10.1186/1756-0500-5-31 doi (DE-627)SPR030280117 (SPR)1756-0500-5-31-e DE-627 ger DE-627 rakwb eng Hu, Qiang verfasserin aut VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. Frequency Pattern (dpeaa)DE-He213 Variant Call (dpeaa)DE-He213 Sequence Call (dpeaa)DE-He213 Variant Call Format (dpeaa)DE-He213 Variant Call Format File (dpeaa)DE-He213 Wang, Dan aut Yan, Li aut Zhao, Hua aut Liu, Song aut Enthalten in BMC Research Notes London, 2008 5(2012), 1 vom: 14. Jan. (DE-627)559431805 (DE-600)2413336-X 1756-0500 nnns volume:5 year:2012 number:1 day:14 month:01 https://dx.doi.org/10.1186/1756-0500-5-31 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2012 1 14 01
allfieldsGer	10.1186/1756-0500-5-31 doi (DE-627)SPR030280117 (SPR)1756-0500-5-31-e DE-627 ger DE-627 rakwb eng Hu, Qiang verfasserin aut VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. Frequency Pattern (dpeaa)DE-He213 Variant Call (dpeaa)DE-He213 Sequence Call (dpeaa)DE-He213 Variant Call Format (dpeaa)DE-He213 Variant Call Format File (dpeaa)DE-He213 Wang, Dan aut Yan, Li aut Zhao, Hua aut Liu, Song aut Enthalten in BMC Research Notes London, 2008 5(2012), 1 vom: 14. Jan. (DE-627)559431805 (DE-600)2413336-X 1756-0500 nnns volume:5 year:2012 number:1 day:14 month:01 https://dx.doi.org/10.1186/1756-0500-5-31 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2012 1 14 01
allfieldsSound	10.1186/1756-0500-5-31 doi (DE-627)SPR030280117 (SPR)1756-0500-5-31-e DE-627 ger DE-627 rakwb eng Hu, Qiang verfasserin aut VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. Frequency Pattern (dpeaa)DE-He213 Variant Call (dpeaa)DE-He213 Sequence Call (dpeaa)DE-He213 Variant Call Format (dpeaa)DE-He213 Variant Call Format File (dpeaa)DE-He213 Wang, Dan aut Yan, Li aut Zhao, Hua aut Liu, Song aut Enthalten in BMC Research Notes London, 2008 5(2012), 1 vom: 14. Jan. (DE-627)559431805 (DE-600)2413336-X 1756-0500 nnns volume:5 year:2012 number:1 day:14 month:01 https://dx.doi.org/10.1186/1756-0500-5-31 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 5 2012 1 14 01
language	English
source	Enthalten in BMC Research Notes 5(2012), 1 vom: 14. Jan. volume:5 year:2012 number:1 day:14 month:01
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format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Frequency Pattern Variant Call Sequence Call Variant Call Format Variant Call Format File
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container_title	BMC Research Notes
authorswithroles_txt_mv	Hu, Qiang @@aut@@ Wang, Dan @@aut@@ Yan, Li @@aut@@ Zhao, Hua @@aut@@ Liu, Song @@aut@@
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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. 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author	Hu, Qiang
spellingShingle	Hu, Qiang misc Frequency Pattern misc Variant Call misc Sequence Call misc Variant Call Format misc Variant Call Format File VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern
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topic_title	VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern Frequency Pattern (dpeaa)DE-He213 Variant Call (dpeaa)DE-He213 Sequence Call (dpeaa)DE-He213 Variant Call Format (dpeaa)DE-He213 Variant Call Format File (dpeaa)DE-He213
topic	misc Frequency Pattern misc Variant Call misc Sequence Call misc Variant Call Format misc Variant Call Format File
topic_unstemmed	misc Frequency Pattern misc Variant Call misc Sequence Call misc Variant Call Format misc Variant Call Format File
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title	VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern
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title_full	VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern
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author_browse	Hu, Qiang Wang, Dan Yan, Li Zhao, Hua Liu, Song
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title_sort	vpa: an r tool for analyzing sequencing variants with user-specified frequency pattern
title_auth	VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern
abstract	Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstractGer	Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstract_unstemmed	Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org. © Hu et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
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title_short	VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern
url	https://dx.doi.org/10.1186/1756-0500-5-31
remote_bool	true
author2	Wang, Dan Yan, Li Zhao, Hua Liu, Song
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up_date	2024-07-03T15:08:46.078Z
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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer) is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. 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VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern

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