ClinVar data parsing

This software repository provides a pipeline for converting raw ClinVar data files into analysis-friendly tab-delimited tables, and also provides these tables for the most recent ClinVar release. Separate tables are generated for genome builds GRCh37 and GRCh38 as well as for mono-allelic variants a...

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Autores principales: Zhang, Xiaolei, Minikel, Eric V., O'Donnell-Luria, Anne H., MacArthur, Daniel G., Ware, James S., Weisburd, Ben
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2017
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473414/
https://www.ncbi.nlm.nih.gov/pubmed/28630944
http://dx.doi.org/10.12688/wellcomeopenres.11640.1
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author Zhang, Xiaolei
Minikel, Eric V.
O'Donnell-Luria, Anne H.
MacArthur, Daniel G.
Ware, James S.
Weisburd, Ben
author_facet Zhang, Xiaolei
Minikel, Eric V.
O'Donnell-Luria, Anne H.
MacArthur, Daniel G.
Ware, James S.
Weisburd, Ben
author_sort Zhang, Xiaolei
collection PubMed
description This software repository provides a pipeline for converting raw ClinVar data files into analysis-friendly tab-delimited tables, and also provides these tables for the most recent ClinVar release. Separate tables are generated for genome builds GRCh37 and GRCh38 as well as for mono-allelic variants and complex multi-allelic variants. Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants. Overall, this work provides ClinVar data in a format that is easier to work with and can be directly loaded into a variety of popular analysis tools such as R, python pandas, and SQL databases.
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spelling pubmed-54734142017-06-19 ClinVar data parsing Zhang, Xiaolei Minikel, Eric V. O'Donnell-Luria, Anne H. MacArthur, Daniel G. Ware, James S. Weisburd, Ben Wellcome Open Res Software Tool Article This software repository provides a pipeline for converting raw ClinVar data files into analysis-friendly tab-delimited tables, and also provides these tables for the most recent ClinVar release. Separate tables are generated for genome builds GRCh37 and GRCh38 as well as for mono-allelic variants and complex multi-allelic variants. Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants. Overall, this work provides ClinVar data in a format that is easier to work with and can be directly loaded into a variety of popular analysis tools such as R, python pandas, and SQL databases. F1000Research 2017-05-23 /pmc/articles/PMC5473414/ /pubmed/28630944 http://dx.doi.org/10.12688/wellcomeopenres.11640.1 Text en Copyright: © 2017 Zhang X et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions.
spellingShingle Software Tool Article
Zhang, Xiaolei
Minikel, Eric V.
O'Donnell-Luria, Anne H.
MacArthur, Daniel G.
Ware, James S.
Weisburd, Ben
ClinVar data parsing
title ClinVar data parsing
title_full ClinVar data parsing
title_fullStr ClinVar data parsing
title_full_unstemmed ClinVar data parsing
title_short ClinVar data parsing
title_sort clinvar data parsing
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473414/
https://www.ncbi.nlm.nih.gov/pubmed/28630944
http://dx.doi.org/10.12688/wellcomeopenres.11640.1
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AT odonnellluriaanneh clinvardataparsing
AT macarthurdanielg clinvardataparsing
AT warejamess clinvardataparsing
AT weisburdben clinvardataparsing

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