[{"_1":2,"_152":-5,"_153":-5},"loaderData",{"_3":4,"_13":14,"_20":21,"_131":132},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":17},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","routes/_layout.r.$namespace.$reponame",{"_22":23,"_24":-5,"_25":11,"_26":11,"_27":28,"_29":30,"_31":-5,"_32":11,"_33":34,"_83":-5,"_84":85,"_124":-5,"_125":11,"_126":17,"_127":11,"_128":-5,"_129":130},"canonicalUrl","https://hub.docker.com/r/animesh1977/variant-caller-16gt/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","animesh1977","reponame","variant-caller-16gt","cloudBuildSource","isAutobuildsAvailable","repo",{"_35":36,"_37":38,"_40":41,"_42":43,"_44":11,"_45":46,"_47":48,"_49":50,"_52":30,"_27":28,"_53":54,"_55":39,"_56":57,"_58":59,"_60":61,"_62":-5,"_63":57,"_64":65,"_66":11,"_67":28,"_68":69,"_74":11,"_75":76,"_80":28,"_81":82},"categories",[],"content_types",[39],"image","date_registered","2019-08-12T16:01:08.515719Z","description","ubuntu 16.04 g++-4.7","is_private","last_updated","2019-08-12T16:08:35.103541Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[51],"application/vnd.docker.container.image.v1+json","name","pull_count",26454,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# Setup\n\n## docker\n```\ngit clone https://github.com/aquaskyline/16GT.git\ncd 16GT\ndocker build --no-cache .\ndocker images\n```\n\n## use the respective \"IMAGE ID\" displayed above as below\n```\ndocker run -it --privileged /bin/bash\n```\n\n## once inside the docker image, index the reference\n```\ncd /16GT/SOAP3-dp\n./soap3-dp-builder \n./BGS-Build .index\n```\n\n\n## variant call using aligned/indexed bam file\n```\ncd /16GT\n./bam2snapshot -i .index -b -o \n./snapshotSnpcaller -i .index -o \nperl txt2vcf.pl .txt

> .vcf\nperl filterVCF.pl .vcf > .filtered.vcf\n```\n\n# 16GT\n16GT is a variant caller utilizing a 16-genotype probabilistic model to unify SNP and indel calling in a single algorithm.\n16GT is easy to use. The default parameters will fit most of the use cases with human genome.\nFor the detailed parameters for each module, please run the module to get an info.\n\n## Quick start\n> Inputs: genome.fa alignments.bam, Output: .vcf\n\n#### 0. Install\n```\ngit clone https://github.com/aquaskyline/16GT\ncd 16GT\nmake\n# Tested in Ubuntu 14.04 and CentOS 6.7 with GCC 4.7.2\n```\n#### 1. Build reference index\n```\ngit clone https://github.com/aquaskyline/SOAP3-dp.git\ncd SOAP3-dp\nmake SOAP3-Builder\nmake BGS-Build\nsoap3-dp-builder genome.fa\nBGS-Build genome.fa.index\n```\n#### 2. Convert BAM to SNAPSHOT\n```\nbam2snapshot -i genome.fa.index -b alignments.bam -o output/prefix\n```\n#### 3. Call \n```\nsnapshotSnpcaller -i genome.fa.index -o output/prefix\nperl txt2vcf.pl output/prefix.txt sampleName genome.fa > .vcf\nperl filterVCF.pl .vcf dbSNP.vcf.gz > .filtered.vcf\n```\n\n## Exome variant calling\n> Inputs: genome.fa alignement.bam region.bed, Outputs: region.bin .vcf\n\n```\nRegionIndexBuilder genome.fa.index region.bed region.bin -bed/-gff\nbam2snapshot -i genome.fa.index -b alignments.bam -o output/prefix -e region.bin\nsnapshotSnpcaller -i genome.fa.index -o output/prefix -e region.bin\n```\n\n## License\nGPLv3\n\n","has_starred","hub_user","immutable_tags_settings",{"_70":11,"_71":72},"enabled","rules",[73],".*","is_automated","permissions",{"_77":17,"_78":11,"_79":11},"read","write","admin","user","storage_size",172035886,"orgData","recentTags",[86],{"_87":39,"_88":89,"_90":91,"_92":93,"_94":95,"_45":113,"_114":89,"_115":28,"_116":51,"_52":117,"_118":119,"_120":104,"_121":113,"_122":61,"_123":17},"content_type","creator",3217692,"full_size",172026882,"id",65055888,"images",[96],{"_97":98,"_99":100,"_101":102,"_103":104,"_105":106,"_107":108,"_109":102,"_110":-5,"_111":91,"_58":61,"_112":-5},"architecture","amd64","digest","sha256:d24ae05993ffb8e888da4ed515c7d5192196e3c7b2c0dc9e039c83d6e6287e8c","features","","last_pulled","2026-09-16T15:12:52.566311649Z","last_pushed","2019-08-12T16:08:35Z","os","linux","os_features","os_version","size","variant","2019-08-12T16:08:34.804664Z","last_updater","last_updater_username","media_type","latest","repository",7540512,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_33":133,"_140":141,"_129":150,"_151":11},{"_35":134,"_37":135,"_40":41,"_42":43,"_44":11,"_45":46,"_47":48,"_49":136,"_52":30,"_27":28,"_53":54,"_55":39,"_56":57,"_58":59,"_60":61,"_62":-5,"_63":57,"_64":65,"_66":11,"_67":28,"_68":137,"_74":11,"_75":139,"_80":28,"_81":82},[],[39],[51],{"_70":11,"_71":138},[73],{"_77":17,"_78":11,"_79":11},"tags",{"_142":59,"_143":-5,"_144":-5,"_145":146},"count","next","previous","results",[147],{"_87":39,"_88":89,"_90":91,"_92":93,"_94":148,"_45":113,"_114":89,"_115":28,"_116":51,"_52":117,"_118":119,"_120":104,"_121":113,"_122":61,"_123":17},[149],{"_97":98,"_99":100,"_101":102,"_103":104,"_105":106,"_107":108,"_109":102,"_110":-5,"_111":91,"_58":61,"_112":-5},[],"canDeleteTags","actionData","errors"]

animesh1977/variant-caller-16gt

Tags for animesh1977/variant-caller-16gt