{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T02:04:12Z","timestamp":1775613852612,"version":"3.50.1"},"posted":{"date-parts":[[2023,12,1]]},"group-title":"Bioinformatics","reference-count":13,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>With the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics \u2013 Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5\/BP6). This tool facilitates large-scale, clinically-focused classification of germline sequence variants in a research setting.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>\n                    AutoGVP is an open-source dockerized workflow implemented in R and freely available on GitHub at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/diskin-lab-chop\/AutoGVP\">https:\/\/github.com\/diskin-lab-chop\/AutoGVP<\/jats:ext-link>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.11.29.569103","type":"posted-content","created":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T15:20:11Z","timestamp":1701444011000},"source":"Crossref","is-referenced-by-count":2,"title":["AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6274-2841","authenticated-orcid":false,"given":"Jung","family":"Kim","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0625-666X","authenticated-orcid":false,"given":"Ammar S.","family":"Naqvi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3478-0784","authenticated-orcid":false,"given":"Ryan J.","family":"Corbett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8535-9730","authenticated-orcid":false,"given":"Rebecca S.","family":"Kaufman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zalman","family":"Vaksman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6782-1442","authenticated-orcid":false,"given":"Miguel A.","family":"Brown","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2032-4358","authenticated-orcid":false,"given":"Daniel P.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2771-2572","authenticated-orcid":false,"given":"Saksham","family":"Phul","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-6883-0691","authenticated-orcid":false,"given":"Zhuangzhuang","family":"Geng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7964-2449","authenticated-orcid":false,"given":"Phillip B.","family":"Storm","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0436-4189","authenticated-orcid":false,"given":"Adam C.","family":"Resnick","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8193-1488","authenticated-orcid":false,"given":"Douglas R.","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2171-3627","authenticated-orcid":false,"given":"Jo Lynne","family":"Rokita","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7200-8939","authenticated-orcid":false,"given":"Sharon J.","family":"Diskin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023120407150844000_2023.11.29.569103v1.1","doi-asserted-by":"publisher","DOI":"10.1002\/humu.23626"},{"key":"2023120407150844000_2023.11.29.569103v1.2","unstructured":"Adam, M.P. et al. (2023) GeneReviews\u00ae University of Washington, Seattle."},{"key":"2023120407150844000_2023.11.29.569103v1.3","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1038\/gim.2018.42","article-title":"The ACMG\/AMP reputable source criteria for the interpretation of sequence variants","volume":"20","year":"2018","journal-title":"Genet. Med"},{"key":"2023120407150844000_2023.11.29.569103v1.4","doi-asserted-by":"crossref","unstructured":"Kim, J. et al. (2021) Pathogenic Germline Variants in Cancer Susceptibility Genes in Children and Young Adults With Rhabdomyosarcoma. JCO Precision Oncology, 5.","DOI":"10.1200\/PO.20.00218"},{"key":"2023120407150844000_2023.11.29.569103v1.5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty897"},{"key":"2023120407150844000_2023.11.29.569103v1.6","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.ajhg.2017.01.004","article-title":"InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines","volume":"100","year":"2017","journal-title":"Am. J. Hum. Genet"},{"key":"2023120407150844000_2023.11.29.569103v1.7","unstructured":"Naqvi, A.S. et al. (2023) diskin-lab-chop\/AutoGVP: Release v0.4.2."},{"key":"2023120407150844000_2023.11.29.569103v1.8","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMsr1406261"},{"key":"2023120407150844000_2023.11.29.569103v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2015.30"},{"key":"2023120407150844000_2023.11.29.569103v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty649"},{"key":"2023120407150844000_2023.11.29.569103v1.11","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1016\/j.ajhg.2023.08.005","article-title":"Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data","volume":"110","year":"2023","journal-title":"Am. J. Hum. Genet"},{"key":"2023120407150844000_2023.11.29.569103v1.12","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq603"},{"key":"2023120407150844000_2023.11.29.569103v1.13","doi-asserted-by":"publisher","DOI":"10.1002\/humu.24051"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.11.29.569103","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T05:35:57Z","timestamp":1768455357000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.11.29.569103"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,1]]},"references-count":13,"URL":"https:\/\/doi.org\/10.1101\/2023.11.29.569103","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1093\/bioinformatics\/btae114","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2023,12,1]]},"subtype":"preprint"}}