Insane in the vembrane: filtering and transforming VCF/BCF files
Abstract Summary We present vembrane as a command line variant call format (VCF)/binary call format (BCF) filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. Vembrane exposes the VCF/BCF file type specification and...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2023-01, Vol.39 (1) |
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| creator | Hartmann, Till Schröder, Christopher Kuthe, Elias Lähnemann, David Köster, Johannes |
| description | Abstract
Summary
We present vembrane as a command line variant call format (VCF)/binary call format (BCF) filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. Vembrane exposes the VCF/BCF file type specification and its inofficial extensions by the annotation tools VEP and SnpEff as Python data structures. vembrane filter enables filtration by Python expressions, requiring only basic knowledge of the Python programming language. vembrane table allows users to generate tables from subsets of annotations or functions thereof. Finally, it is fast, by using pysam and relying on lazy evaluation.
Availability and implementation
Source code and installation instructions are available at github.com/vembrane/vembrane (doi: 10.5281/zenodo.7003981).
Supplementary information
Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btac810 |
| format | Article |
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Summary
We present vembrane as a command line variant call format (VCF)/binary call format (BCF) filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. Vembrane exposes the VCF/BCF file type specification and its inofficial extensions by the annotation tools VEP and SnpEff as Python data structures. vembrane filter enables filtration by Python expressions, requiring only basic knowledge of the Python programming language. vembrane table allows users to generate tables from subsets of annotations or functions thereof. Finally, it is fast, by using pysam and relying on lazy evaluation.
Availability and implementation
Source code and installation instructions are available at github.com/vembrane/vembrane (doi: 10.5281/zenodo.7003981).
Supplementary information
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4811</identifier><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btac810</identifier><identifier>PMID: 36519840</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Annotations ; Applications Note ; Availability ; Bioinformatics ; Data structures ; Filtration ; Format ; Genetic Variation ; Humans ; Mental Disorders ; Programming Languages ; Python ; Software ; Source code</subject><ispartof>Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)</ispartof><rights>The Author(s) 2022. Published by Oxford University Press. 2022</rights><rights>The Author(s) 2022. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c484t-c07a29c6a9840db1ff8d7f3db74e64c41495360790b29d74fda27f07df0bf2cc3</citedby><cites>FETCH-LOGICAL-c484t-c07a29c6a9840db1ff8d7f3db74e64c41495360790b29d74fda27f07df0bf2cc3</cites><orcidid>0000-0002-9138-4112 ; 0000-0002-6993-347X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825764/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825764/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36519840$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hartmann, Till</creatorcontrib><creatorcontrib>Schröder, Christopher</creatorcontrib><creatorcontrib>Kuthe, Elias</creatorcontrib><creatorcontrib>Lähnemann, David</creatorcontrib><creatorcontrib>Köster, Johannes</creatorcontrib><title>Insane in the vembrane: filtering and transforming VCF/BCF files</title><title>Bioinformatics (Oxford, England)</title><addtitle>Bioinformatics</addtitle><description>Abstract
Summary
We present vembrane as a command line variant call format (VCF)/binary call format (BCF) filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. Vembrane exposes the VCF/BCF file type specification and its inofficial extensions by the annotation tools VEP and SnpEff as Python data structures. vembrane filter enables filtration by Python expressions, requiring only basic knowledge of the Python programming language. vembrane table allows users to generate tables from subsets of annotations or functions thereof. Finally, it is fast, by using pysam and relying on lazy evaluation.
Availability and implementation
Source code and installation instructions are available at github.com/vembrane/vembrane (doi: 10.5281/zenodo.7003981).
Supplementary information
Supplementary data are available at Bioinformatics online.</description><subject>Annotations</subject><subject>Applications Note</subject><subject>Availability</subject><subject>Bioinformatics</subject><subject>Data structures</subject><subject>Filtration</subject><subject>Format</subject><subject>Genetic Variation</subject><subject>Humans</subject><subject>Mental Disorders</subject><subject>Programming Languages</subject><subject>Python</subject><subject>Software</subject><subject>Source code</subject><issn>1367-4811</issn><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqNkc1OxCAUhYnR-P8KpokbN3WgQGldGLVxdJJJ3KhbQikopoUR2kl8e2lmnIyuXAGX7557Tw4AZwheIljiSW2csdr5TvRGhkndC1kguAMOEc5ZSgqEdrfuB-AohA8IIYU03wcHOKeoLAg8BDczG4RVibFJ_66SpepqH99XiTZtr7yxb4mwTdLHYhjHjYXXajq5q6YjosIJ2NOiDep0fR6Dl-n9c_WYzp8eZtXtPJWkIH0qIRNZKXMxjm1qpHXRMI2bmhGVE0kQKSnOISthnZUNI7oRGdOQNRrWOpMSH4Prle5iqDvVSGXjTi1feNMJ_8WdMPz3jzXv_M0teVlklOUkClysBbz7HFToeWeCVG0b7boh8IxRUlAGEYro-R_0ww3eRnscI4xplpWMRipfUdK7ELzSm2UQ5GNI_HdIfB1SbDzbtrJp-0klAmgFuGHxX9Fv_QylBA</recordid><startdate>20230101</startdate><enddate>20230101</enddate><creator>Hartmann, Till</creator><creator>Schröder, Christopher</creator><creator>Kuthe, Elias</creator><creator>Lähnemann, David</creator><creator>Köster, Johannes</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7TO</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-9138-4112</orcidid><orcidid>https://orcid.org/0000-0002-6993-347X</orcidid></search><sort><creationdate>20230101</creationdate><title>Insane in the vembrane: filtering and transforming VCF/BCF files</title><author>Hartmann, Till ; Schröder, Christopher ; Kuthe, Elias ; Lähnemann, David ; Köster, Johannes</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c484t-c07a29c6a9840db1ff8d7f3db74e64c41495360790b29d74fda27f07df0bf2cc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Annotations</topic><topic>Applications Note</topic><topic>Availability</topic><topic>Bioinformatics</topic><topic>Data structures</topic><topic>Filtration</topic><topic>Format</topic><topic>Genetic Variation</topic><topic>Humans</topic><topic>Mental Disorders</topic><topic>Programming Languages</topic><topic>Python</topic><topic>Software</topic><topic>Source code</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hartmann, Till</creatorcontrib><creatorcontrib>Schröder, Christopher</creatorcontrib><creatorcontrib>Kuthe, Elias</creatorcontrib><creatorcontrib>Lähnemann, David</creatorcontrib><creatorcontrib>Köster, Johannes</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hartmann, Till</au><au>Schröder, Christopher</au><au>Kuthe, Elias</au><au>Lähnemann, David</au><au>Köster, Johannes</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Insane in the vembrane: filtering and transforming VCF/BCF files</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><addtitle>Bioinformatics</addtitle><date>2023-01-01</date><risdate>2023</risdate><volume>39</volume><issue>1</issue><issn>1367-4811</issn><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>Abstract
Summary
We present vembrane as a command line variant call format (VCF)/binary call format (BCF) filtering tool that consolidates and extends the filtering functionality of previous software to meet any imaginable filtering use case. Vembrane exposes the VCF/BCF file type specification and its inofficial extensions by the annotation tools VEP and SnpEff as Python data structures. vembrane filter enables filtration by Python expressions, requiring only basic knowledge of the Python programming language. vembrane table allows users to generate tables from subsets of annotations or functions thereof. Finally, it is fast, by using pysam and relying on lazy evaluation.
Availability and implementation
Source code and installation instructions are available at github.com/vembrane/vembrane (doi: 10.5281/zenodo.7003981).
Supplementary information
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>36519840</pmid><doi>10.1093/bioinformatics/btac810</doi><orcidid>https://orcid.org/0000-0002-9138-4112</orcidid><orcidid>https://orcid.org/0000-0002-6993-347X</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Bioinformatics (Oxford, England), 2023-01, Vol.39 (1) |
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| language | eng |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Annotations Applications Note Availability Bioinformatics Data structures Filtration Format Genetic Variation Humans Mental Disorders Programming Languages Python Software Source code |
| title | Insane in the vembrane: filtering and transforming VCF/BCF files |
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