{"id":13752028,"url":"https://github.com/AstraZeneca-NGS/VarDict","last_synced_at":"2025-05-09T18:33:03.316Z","repository":{"id":18652308,"uuid":"21859333","full_name":"AstraZeneca-NGS/VarDict","owner":"AstraZeneca-NGS","description":"VarDict","archived":false,"fork":false,"pushed_at":"2024-01-05T14:06:13.000Z","size":1496,"stargazers_count":186,"open_issues_count":37,"forks_count":61,"subscribers_count":52,"default_branch":"master","last_synced_at":"2024-08-03T09:03:30.170Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AstraZeneca-NGS.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2014-07-15T12:50:23.000Z","updated_at":"2024-07-13T05:38:56.000Z","dependencies_parsed_at":"2024-08-03T09:13:12.919Z","dependency_job_id":null,"html_url":"https://github.com/AstraZeneca-NGS/VarDict","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca-NGS%2FVarDict","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca-NGS%2FVarDict/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca-NGS%2FVarDict/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca-NGS%2FVarDict/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AstraZeneca-NGS","download_url":"https://codeload.github.com/AstraZeneca-NGS/VarDict/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224876976,"owners_count":17384699,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-03T09:00:58.340Z","updated_at":"2024-11-16T04:32:14.033Z","avatar_url":"https://github.com/AstraZeneca-NGS.png","language":"Perl","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"    This is the Final Version of VarDict. No longer maintained.\n\nVarDict\n=======\n\nVarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files.\nVarDict implements several novel features such as amplicon bias aware variant calling from targeted\nsequencing experiments, rescue of long indels by realigning bwa soft clipped reads and better scalability\nthan many Java based variant callers.\n\nDue to the philosophy of VarDict in calling \"everything\", several downstream strategies have been developed\nto filter variants to for example the most likely cancer driving events. These strategies are based on evidence\nin different databases and/or quality metrics. http://bcb.io/2016/04/04/vardict-filtering/ provides an overview of \nhow to develop further filters for VarDict. The script at https://github.com/AstraZeneca-NGS/VarDict/blob/master/vcf2txt.pl \ncan be used to put the variants into a context by including information from dbSNP, Cosmic and ClinVar. We are open to \nsuggestions from the community on how to best narrow down to the variants of most interest. \n\nA Java based drop-in replacement for vardict.pl is being developed at https://github.com/AstraZeneca-NGS/VarDictJava. \nThe Java implementation is approximately 10 times faster than the original \nPerl implementation and does not depend\non samtools\n\nTo enable amplicon aware variant calling (single sample mode only; not supported in paired variant calling),\nplease make sure the bed file has 8 columns with the 7th and 8th columns containing the insert interval \n(therefore subset of the 2nd and 3rd column interval). The bed files typically look similar to the below two\noverlapping intervals:\n\n``chr1    115247094       115247253       NRAS    0       .       115247117       115247232``\n\n``chr1    115247202       115247341       NRAS    0       .       115247224       115247323``\n\nFor more information on amplicon aware calling please see https://github.com/AstraZeneca-NGS/VarDict/wiki/Amplicon-Mode-in-VarDict\n\nVarDict is fully integrated in e.g. bcbio-nextgen, see https://github.com/chapmanb/bcbio-nextgen\n\nPlease cite VarDict:\n\nLai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, Johnson J, Dougherty B, Barrett JC, and Dry JR.  VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Res. 2016, pii: gkw227.\n\nThe link to is article can be accessed through: http://nar.oxfordjournals.org/cgi/content/full/gkw227?ijkey=Tk8eKQcYwNlQRNU\u0026keytype=ref\n\nCoded by Zhongwu Lai 2014.\n\nRequirements\n------------\n\n- Perl (uses /usr/bin/env perl)\n- R (uses /usr/bin/env R)\n- samtools (must be in path, not required if using the Java implementation in place of vardict.pl)\n\nQuick start\n-----------\n\nMake sure the VarDict folder (scripts ``vardict.pl``, ``vardict``, ``testsomatic.R``, ``teststrandbias.R``, ``var2vcf_valid.pl`` and ``var2vcf_paired.pl``) is in path before running the following commands.\n\n- Running in single sample mode::\n\n         AF_THR=\"0.01\" # minimum allele frequency\n         vardict -G /path/to/hg19.fa -f $AF_THR -N sample_name -b /path/to/my.bam -c 1 -S 2 -E 3 -g 4 /path/to/my.bed | teststrandbias.R | var2vcf_valid.pl -N sample_name -E -f $AF_THR\n\n\n- Paired variant calling::\n\n         AF_THR=\"0.01\" # minimum allele frequency\n         vardict -G /path/to/hg19.fa -f $AF_THR -N tumor_sample_name -b \"/path/to/tumor.bam|/path/to/normal.bam\" -c 1 -S 2 -E 3 -g 4 /path/to/my.bed | testsomatic.R | var2vcf_paired.pl -N \"tumor_sample_name|normal_sample_name\" -f $AF_THR\n\n\nContributors\n------------\n\n- `Zhongwu Lai`_, AstraZeneca\n.. _Zhongwu Lai: https://github.com/zhongwulai\n- `Miika Ahdesmaki`_, AstraZeneca\n.. _Miika Ahdesmaki: https://github.com/mjafin\n- `Brad Chapman`_, Harvard School of Public Health\n.. _Brad Chapman: https://github.com/chapmanb\n\n\nLicense\n-------\n\nThe code is freely available under the `MIT license`_.\n\n.. _MIT license: http://www.opensource.org/licenses/mit-license.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAstraZeneca-NGS%2FVarDict","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FAstraZeneca-NGS%2FVarDict","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAstraZeneca-NGS%2FVarDict/lists"}