What is NVIDIA Parabricks?

NVIDIA Parabricks is an accelerated compute framework that supports applications across the genomics industry, primarily supporting analytical workflows for DNA, RNA, and somatic mutation detection applications. With industry leading compute times, Parabricks rapidly converts a FASTQ file to a VCF using multiple, industry validated variant callers and also includes the ability to QC those variants. As Parabricks is based upon publicly available tools, results are easy to verify and combine with other publicly available datasets.

More information is available on the Parabricks Product Page.\nDetailed installation, usage, and tuning information is available in the Parabricks user guide.

Answers to common questions can be found on the Parabricks developer forum.

The Parabricks docker image can be obtained by running the following command:

\n\">

$ docker pull nvcr.io/nvidia/clara/clara-parabricks:<TAG>\n

An example run of the fq2bam tool using the container will be as follow:

and all the outputs go to .\n$ docker run --rm --gpus all -v :/workdir \\\n-v :/outputdir \\\n-v :/raid/myrun -w /workdir \\\nnvcr.io/nvidia/clara/clara-parabricks: \\\npbrun fq2bam \\\n--ref /workdir/${REFERENCE_FILE} \\\n--in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2} \\\n--knownSites /workdir/${KNOWN_SITES_FILE} \\\n--out-bam /outputdir/${OUTPUT_BAM} \\\n--out-recal-file /outputdir/${OUTPUT_RECAL_FILE}\n\">

#This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.\n$ docker run --rm --gpus all -v <INPUT_DIR>:/workdir \\\n-v <OUTPUT_DIR>:/outputdir \\\n-v <TMP_DIR>:/raid/myrun -w /workdir \\\nnvcr.io/nvidia/clara/clara-parabricks:<TAG> \\\npbrun fq2bam \\\n--ref /workdir/${REFERENCE_FILE} \\\n--in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2}  \\\n--knownSites /workdir/${KNOWN_SITES_FILE} \\\n--out-bam /outputdir/${OUTPUT_BAM} \\\n--out-recal-file /outputdir/${OUTPUT_RECAL_FILE}\n

NOTE: These instructions and commands are valid for Parabricks versions 4.0.1-1 and above only. For earlier versions, please visit Parabricks user guides for each specific older version.\nYou will need an installer for versions prior to v4.0.1-1. Instructions for this are also in the Parabricks user guides.

License

By pulling and using the Parabricks container, you accept the terms and conditions of the NVIDIA AI Product Agreement. For enterprise support, register for a free evaluation license to try NVIDIA AI Enterprise on your compatible, on-premises system or on the cloud.

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With industry leading compute times, Parabricks rapidly converts a FASTQ file to a VCF using multiple, industry validated variant callers and also includes the ability to QC those variants. As Parabricks is based upon publicly available tools, results are easy to verify and combine with other publicly available datasets.\n\n\nMore information is available on the [Parabricks Product Page](https://www.nvidia.com/en-us/industries/healthcare-life-sciences/genomics/).\nDetailed installation, usage, and tuning information is available in the [Parabricks user guide](https://docs.nvidia.com/clara/#parabricks).\n\nAnswers to common questions can be found on the [Parabricks developer forum](https://forums.developer.nvidia.com/c/healthcare/parabricks/290).\n\n\nThe Parabricks docker image can be obtained by running the following command:\n\n\n $ docker pull nvcr.io/nvidia/clara/clara-parabricks:\n\n\nAn example run of the fq2bam tool using the container will be as follow:\n\n\n #This command assumes all the inputs are in and all the outputs go to .\n $ docker run --rm --gpus all -v :/workdir \\\n -v :/outputdir \\\n -v :/raid/myrun -w /workdir \\\n nvcr.io/nvidia/clara/clara-parabricks: \\\n pbrun fq2bam \\\n --ref /workdir/${REFERENCE_FILE} \\\n --in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2} \\\n --knownSites /workdir/${KNOWN_SITES_FILE} \\\n --out-bam /outputdir/${OUTPUT_BAM} \\\n --out-recal-file /outputdir/${OUTPUT_RECAL_FILE}\n\n\n\n\nNOTE: These instructions and commands are valid for Parabricks versions 4.0.1-1 and above only. For earlier versions, please visit [Parabricks user guides](https://docs.nvidia.com/clara/#parabricks) for each specific older version.\nYou will need an installer for versions prior to v4.0.1-1. Instructions for this are also in the [Parabricks user guides](https://docs.nvidia.com/clara/#parabricks).\n\n\n\n# License\n\nBy pulling and using the Parabricks container, you accept the terms and conditions of the [NVIDIA AI Product Agreement](https://www.nvidia.com/en-us/data-center/products/nvidia-ai-enterprise/eula/). 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This function remembers how far the user has scrolled on the current session across the website's sub-pages.","dmn_chk_-xxxxxxxxxxxx","com","Posthog Analytics","_hly_vid","This cookie _hly_vid is used to record website and server performance with each visit to the site. The data is aggregated and analyzed; therefore, it remains anonymous upon use.","_cs_id","blogs.nvidia.com","_session_id","resources.nvidia.com","This cookie creates an interim session ID used as an in-session user ID.\n","s_cc","This cookie is associated with the Adobe Site Catalyst. It determines whether cookies are enabled in the web browser.","_hjSessionUser_xxxxxx","Hotjar cookie that is set when a user first lands on a page with the Hotjar script. It is used to persist the Hotjar User ID, unique to that site on the browser. This ensures that behavior in subsequent visits to the same site will be attributed to the same user ID.","_hjHasCachedUserAttributes","This cookie name is associated with Hotjar which is used to know whether the data set in _hjUserAttributes Local Storage item is up to date or not.","s_ppv","This cookie is associated with Adobe Analytics site tracking and is used to measure a user's scroll activity to see how much of a page they view before moving to another page.","nv.referrerHref","This domain is owned by NVIDIA Corporation which provides information about the company, its products, solutions, industries, news, events, and career opportunities.","_gid","This cookie name is associated with Google Universal Analytics. This appears to be a new cookie and as of Spring 2017 no information is available from Google. It appears to store and update a unique value for each page visited.","__sec_crid","_hjTLDTest","When the Hotjar script executes we try to determine the most generic cookie path we should use, instead of the page hostname. This is done so that cookies can be shared across subdomains (where applicable). To determine this, we try to store the _hjTLDTest cookie for different URL substring alternatives until it fails. 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These cookies are required for the site to function and cannot be turned off.",[1181,1182,1183,1184,1185,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1196,1197,1198,1199,1200,1201,1202,1203,1204,1205,1206,1207,1208,1209,1210,1211,1212,1213,1214,1215,1216,1217,1218,1219,1220,1221,1222,1223,1224,1225,1226,1227,1228,1229,1230,1231,1232,1233,1234,1235,1236,1237,1238,1239,1240,1241,1242,1243,1244,1245,1246,1247,1248,1249,1250,1251,1252,1253,1254,1255,1256,1257,1258,1259,1260,1261,1262,1263,1264,1265,1266,1267,1268,1269],[1033,1034,1035,1036,1037,1038,1039,1040,1041,1042,1043,1044,1045,1046,1047,1048,1049,1050,1051,1052,1053,1054,1055,1056,1057],{"_524":1176,"_92":1176,"_91":526,"_498":1177},{"_524":1170,"_92":1170,"_91":526,"_498":1171},{"_524":1158,"_92":1158,"_91":526,"_498":1159},{"_524":1155,"_92":1155,"_91":526,"_498":1156},{"_524":1152,"_92":1152,"_91":526,"_498":1153},{"_524":1147,"_92":1147,"_91":526,"_498":1148},{"_524":1142,"_92":1142,"_91":526,"_498":1143},{"_524":600,"_92":600,"_91":526,"_498":1139},{"_524":1135,"_92":1135,"_91":526,"_498":1136},{"_524":588,"_92":588,"_91":526,"_498":1133},{"_524":583,"_92":583,"_91":526,"_498":1131},{"_524":1126,"_92":1126,"_91":526,"_498":1127},{"_524":1121,"_92":1121,"_91":526,"_498":1122},{"_524":1116,"_92":1116,"_91":526,"_498":1117},{"_524":1113,"_92":1113,"_91":526,"_498":1114},{"_524":557,"_92":557,"_91":526,"_498":1111},{"_524":1103,"_92":1103,"_91":526,"_498":1104},{"_524":733,"_92":733,"_91":526,"_498":1097},{"_524":1091,"_92":1091,"_91":526,"_498":1092},{"_524":1087,"_92":1087,"_91":526,"_498":1088},{"_524":1082,"_92":1082,"_91":526,"_498":1083},{"_524":1078,"_92":1078,"_91":526,"_498":1079},{"_524":1073,"_92":1073,"_91":526,"_498":1074},{"_524":728,"_92":728,"_91":526,"_498":1066},{"_524":1058,"_92":1058,"_91":526,"_498":1059},"pexels.com",[1060,1061],{"_269":1064,"_531":1058,"_532":26,"_91":1065},{"_269":1062,"_531":1058,"_532":135,"_91":1063},"_cfuvid","Pexels provides high quality and completely free stock photos licensed under the Pexels license. These photos are often used for personal and commercial purposes.","__cf_bm","This is a CloudFoundry cookie",[1067,1068],{"_269":1071,"_531":728,"_532":26,"_91":1072},{"_269":1069,"_531":728,"_532":26,"_91":1070},"CookieConsentPolicy","Used to apply end-user cookie consent preferences set by our client-side utility.","LSKey-c$CookieConsentPolicy","Custom- Short Duration. Unique ID of an Enquiry- used to validate access to case, and load exisiting data.\n","www.recaptcha.net",[1075],{"_269":1076,"_531":1073,"_532":26,"_91":1077},"_GRECAPTCHA","This domain is used by Google reCAPTCHA, which provides spam protection services to websites by detecting if a user is a human or a bot.","api2.hcaptcha.com",[1080],{"_269":1081,"_531":1078,"_532":26,"_91":566},"__cflb","instagram.com",[1084],{"_269":1085,"_531":1082,"_532":26,"_91":1086},"csrftoken","Instagram is a social networking service owned by Facebook, Inc. It's designed for sharing photos and videos from a smartphone. The service also uses cookies for various purposes, including analytics, personalization, and advertising.","readme.io",[1089],{"_269":1064,"_531":1087,"_532":26,"_91":1090},"The __cf_bm cookie is a cookie necessary to support Cloudflare Bot Management, currently in private beta. As part of our bot management service, this cookie helps manage incoming traffic that matches criteria associated with bots.","nvidiacorp.us-5.evergage.com",[1093,1094],{"_269":1096,"_531":1091,"_532":26,"_91":566},{"_269":1095,"_531":1091,"_532":26,"_91":566},"AWSALBTG","AWSALBTGCORS",[1098,1099],{"_269":1101,"_531":733,"_532":26,"_91":1102},{"_269":1100,"_531":733,"_532":26,"_91":566},"ak_bmsc","bm_mi","This domain is likely associated with NVIDIA's partner program, which could involve marketing, sales, and support services for partners.","app.hushly.com",[1105,1106,1107],{"_269":1110,"_531":1103,"_532":26,"_91":566},{"_269":1109,"_531":1103,"_532":135,"_91":566},{"_269":1108,"_531":1103,"_532":26,"_91":566},"AWSALBCORS","JSESSIONID","AWSALB",[1112],{"_269":1064,"_531":557,"_532":26,"_91":1065},"hcaptcha.com",[1115],{"_269":1064,"_531":1113,"_532":26,"_91":1065},"tracking.intentsify.io",[1118],{"_269":1119,"_531":1116,"_532":26,"_91":1120},"userId","Used to track usage of the embedded video player.","static.reo.dev",[1123],{"_269":1124,"_531":1121,"_532":26,"_91":1125},"cookietest","Common cookie name could have a number of different origins. Where this is first party and a session cookie, its most likely to do with checking to see if the browser is set to block or allow cookies.","www.datadoghq-browser-agent.com",[1128],{"_269":1129,"_531":1126,"_532":26,"_91":1130},"dd_cookie_test_","dd_cookie_test",[1132],{"_269":1064,"_531":583,"_532":26,"_91":1065},[1134],{"_269":1064,"_531":588,"_532":26,"_91":1065},"mynvidia.force.com",[1137,1138],{"_269":1071,"_531":1135,"_532":26,"_91":1072},{"_269":1069,"_531":1135,"_532":26,"_91":1070},[1140],{"_269":1141,"_531":600,"_532":26,"_91":609},"VISITOR_PRIVACY_METADATA","prod.cloudmatchbeta.nvidiagrid.net",[1144],{"_269":1145,"_531":1142,"_532":135,"_91":1146},"SERVERID","Usually used for load balancing. Identifies the server that delivered the last page to the browser. Associated with the HAProxy Load Balancer software.","dosa-prd.azurewebsites.net",[1149],{"_269":1150,"_531":1147,"_532":26,"_91":1151},"access_token","This cookie is used to obtain the permissions for users of the portal to allow for API access in order to retrieve information required to perform portal functions.","w.hcaptcha.com",[1154],{"_269":1064,"_531":1152,"_532":26,"_91":1065},"cdn.readme.io",[1157],{"_269":1064,"_531":1155,"_532":26,"_91":1065},"queue-it.net",[1160,1161,1162,1163,1164],{"_269":1169,"_531":1158,"_532":26,"_91":526},{"_269":1168,"_531":1158,"_532":26,"_91":526},{"_269":1167,"_531":1158,"_532":26,"_91":526},{"_269":1166,"_531":1158,"_532":26,"_91":526},{"_269":1165,"_531":1158,"_532":26,"_91":526},"Queue-it-{queueId}","Queue-it-{dmonvidia }________{eventId}","Queue-it-token","queueitsoftblock_{queueId}","Queue-it-{nvidia}________{eventId}","api.hcaptcha.com",[1172,1173],{"_269":1175,"_531":1170,"_532":26,"_91":566},{"_269":1081,"_531":1170,"_532":26,"_91":1174},"This domain is associated with hCaptcha, a service that provides CAPTCHA and reCAPTCHA alternatives for user verification and bot protection.","hmt_id","vimeo.com",[1178,1179],{"_269":1064,"_531":1176,"_532":26,"_91":1065},{"_269":1062,"_531":1176,"_532":135,"_91":1180},"This domain is owned by Vimeo. 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As part of our bot management service, this cookie helps manage incoming traffic that matches criteria associated with bots.\nThis is a CloudFoundry cookie","OptanonConsent","nvid.nvidia.com","This cookie is set by the cookie compliance solution from OneTrust. It stores information about the categories of cookies the site uses and whether visitors have given or withdrawn consent for the use of each category. This enables site owners to prevent cookies in each category from being set in the users browser, when consent is not given. The cookie has a normal lifespan of one year, so that returning visitors to the site will have their preferences remembered. It contains no information that can identify the site visitor.","events.nvidia.com","This cookie is associated with the Amazon Web Services Elastic Load Balancing functionality for routing client request on the server.Used to attribute commission to affiliates when you arrive at the website from an affiliate referral link. It is set when you click on one of our links and used to let the advertiser and us know the website from which you came.","sessionid","This is a very generic cookie name that may have different purposes on different sites, but generally it will be some kind of anonymous session identifier.","_csrf","This cookie is used to prevent Cross-Site Request Forgery (CSRF) attacks, ensuring that each request made to the server is from the user's browser and is intentional.","enterprise-support.nvidia.com","Used to apply end-user cookie consent preferences set by our client-side utility.Custom- Short Duration. Unique ID of an Enquiry- used to validate access to case, and load exisiting data.\n","renderCtx","academicgrants.nvidia.com","Used to store site parameters in the session for reuse across requests by a single client for functionality and performance reasons.","ph_phc_yQgAEdJJkVpI24NdSRID2mor1x1leRpDoC9yZ9mfXal_posthog","The PostHog ph_phc_xxx cookie is a session cookie used for identifying and tracking visitors on websites, helping us understand user behavior and website performance.","This cookie is managed by AWS and is used for load balancing.Used to attribute commission to affiliates when you arrive at the website from an affiliate referral link. It is set when you click on one of our links and used to let the advertiser and us know the website from which you came.","This cookie is associated with Akamai and is used to differentiate between traffic from humans and bots.","OptanonAlertBoxClosed","docs.ngc.nvidia.com","This cookie is set by websites using certain versions of the cookie law compliance solution from OneTrust. It is set after visitors have seen a cookie information notice and in some cases only when they actively close the notice down. It enables the website not to show the message more than once to a user. The cookie has a normal lifespan of one year and contains no personal information.","nv_co","__uxq412__ses.88c1","investor.nvidia.com","learn.learn.nvidia.com","This cookie is associated with the Amazon Web Services Elastic Load Balancing functionality for routing client request on the server.","pctrk","Used to count page views by unauthenticated users against license usage.","bm_s","bpazaws52gukakzc__ctrl0_ctl36_uccaptcha","bm_sv","store.nvidia.com","The __cf_bm cookie is a cookie necessary to support Cloudflare Bot Management, currently in private beta. As part of our bot management service, this cookie helps manage incoming traffic that matches criteria associated with bots.\n","This cookie name is used by DataDog to determine if cookies are supported on the website.dd_cookie_test","AMP_TLDTEST_xxxxxxxx","SESSlsd","This cookie is likely to be a session identifier used to maintain user session state across page requests.","mboxEdgeCluster","This cookie name is associated with Adobe Target which is used to communicate the correct edge cluster to at.js so that Target profiles can stay in sync as users navigate across a site.","_biz_pendingA","_rdt_em","This cookie name is associated with Reddit which is used to manage session state and user interactions.","megaNavCollapsed","_abck","The _abck cookie is associated with Akamai's Bot Manager, which is used to prevent fraud and abuse by safeguarding online interactions and detecting irregularities that could suggest malicious activity, such as bot-driven attacks or hacking attempts.","AMP_TEST","This cookie name AMP_TEST is used for internal analytics by the website operator, necessary for the functionality of the website's chat-box function, and to check whether the cookie storage is working properly.","idccsrf","This cookie name is associated with Salesforce which is used to track CrossSiteRequestForgery validation for certain single sign-on (SSO) flows.","_biz_flagsA","This cookie is used to remember users' settings as well as for authentication and analytics.","ApplicationGatewayAffinity","partners.nvidia.com","This cookie is used to maintain a user session by the server in a load balanced environment, to ensure the user has a consistent experience.","AMP_TEST_xxxxxxxx","bm_lso","This cookie name is associated with Akamai which is used to load the site as quickly as possible and to recognize bots.","SSESS###########","This cookie is likely to be a session cookie used to maintain an anonymized user session by the server in a secure environment, often seen in sites built with the Drupal content management system.","nvdeveloper.nvidia.com","__uxq412__id.88c1","QueueITAccepted-SDFrts345E-V3_{eventId}","TEST_AMCV_COOKIE_WRITE","This cookie is used to test whether cookies are enabled in the browser. It is a temporary cookie used to determine if the browser accepts cookies.","session","This cookie is typically used to maintain an anonymized user session by the server.","XSRF-TOKEN","This cookie is written to help with site security in preventing Cross-Site Request Forgery attacks.This cookie helps with site security in preventing Cross-Site Request Forgery attacks.","AWS ELB application load balancer","This cookie is associated with Akamai. It is used to analyse traffic to determine if it is automated traffic generated by bots or a human user.","bpazaws52gukakzc__ctrl0_ctl78_list_ctl09_systemcaptcha","PHPSESSID","PHP session cookie associated with embedded content from this domain.\n","base.manager.learn.nvidia.com","login_session","bm_ss","This cookie is used to help protect websites from automated bot traffic.","AWS ELB application load balancerUsed to attribute commission to affiliates when you arrive at the website from an affiliate referral link. It is set when you click on one of our links and used to let the advertiser and us know the website from which you came.","_devzone_session","This cookie is likely used to maintain a user session on the website by the server. It is common for session identifiers to be used to keep users logged in and track their interaction with the site during a session.","_cs_c","The cookie is used by Content Square to save the user consent to be tracked.","bm_sz","This cookie is used by Akamai to optimize site performance and security. It is typically associated with the delivery of web content and services.","vcalliance.nvidia.com","ASP.NET_SessionId","General purpose platform session cookie, used by sites written with Microsoft .NET based technologies. 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