This tool recalibrates quality scores in a BAM file using the report generated by the bqsr [link] tool. This should be applied after alignment but before variant calling to maximize final accuracy in variant calling, as recommended by GATK best practices.\nPlease note that the applybqsr tool will use at most two GPUs.

For further information visit the applybqsr help page.

Quick Start

and all the outputs go to .\n$ docker run --rm --gpus all --volume :/workdir --volume :/outputdir\n -w /workdir \\\n nvcr.io/nvidia/clara/clara-parabricks: \\\n pbrun applybqsr \\\n --ref /workdir/${REFERENCE_FILE} \\\n --in-bam /workdir/${INPUT_BAM} \\\n --in-recal-file /workdir/${INPUT_RECAL_FILE} \\\n --out-bam /outputdir/${OUTPUT_BAM}\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 --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir\n    -w /workdir \\\n    nvcr.io/nvidia/clara/clara-parabricks:<VERSION-TAG> \\\n    pbrun applybqsr \\\n    --ref /workdir/${REFERENCE_FILE} \\\n    --in-bam /workdir/${INPUT_BAM} \\\n    --in-recal-file /workdir/${INPUT_RECAL_FILE}  \\\n    --out-bam /outputdir/${OUTPUT_BAM}\n

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We and our advertising partners will use this information to make our websites and the advertising displayed on it, more relevant to your interests.",5,[492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526],[364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380],{"_381":488,"_91":488,"_90":383,"_354":489},{"_381":483,"_91":483,"_90":383,"_354":484},{"_381":479,"_91":479,"_90":383,"_354":480},{"_381":474,"_91":474,"_90":383,"_354":475},{"_381":469,"_91":469,"_90":383,"_354":470},{"_381":457,"_91":457,"_90":383,"_354":458},{"_381":445,"_91":445,"_90":383,"_354":446},{"_381":440,"_91":440,"_90":383,"_354":441},{"_381":429,"_91":429,"_90":383,"_354":430},{"_381":424,"_91":424,"_90":383,"_354":425},{"_381":419,"_91":419,"_90":383,"_354":420},{"_381":414,"_91":414,"_90":383,"_354":415},{"_381":409,"_91":409,"_90":383,"_354":410},{"_381":404,"_91":404,"_90":383,"_354":405},{"_381":399,"_91":399,"_90":383,"_354":400},{"_381":392,"_91":392,"_90":383,"_354":393},{"_381":382,"_91":382,"_90":383,"_354":384},"hostName","amazon-adsystem.com","",[385,386],{"_232":391,"_388":382,"_389":26,"_90":390},{"_232":387,"_388":382,"_389":26,"_90":390},"ad-privacy","host","isSession","This domain is owned by online retailer Amazon and is used as part of its affiliate marketing programme.","ad-id","doubleclick.net",[394,395],{"_232":398,"_388":392,"_389":26,"_90":397},{"_232":396,"_388":392,"_389":26,"_90":397},"IDE","This domain is owned by Doubleclick (Google). 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It stores a unique visitor identifier, and uses an organisation identifier to allow a company to track users across their domains and services.This is a pattern type cookie name associated with Adobe Marketing Cloud. It stores a unique visitor identifier, and uses an organisation identifier.","kndctr_F207D74D549850760A4C98C6_AdobeOrg_identity","_rdt_pn","www.nvidia.com","This cookie name is associated with www.mind.org.uk which is used for marketing purposes.","ai-podcast.nvidia.com","This cookie is used to identify the user's session on the website and is often associated with analytics or personalization.","_gcl_au","Used by Google AdSense for experimenting with advertisement efficiency across websites using their services","_mkto_trk","This cookie is associated with an email marketing service provided by Marketo. This tracking cookie allows a website to link visitor behaviour to the recipient of an email marketing campaign, to measure campaign effectiveness.","_gat_gtag_UA_140825383_2","Google Analytics","_zitok","This cookie name is associated with ZoomInfo which is used to maintain a unique visitor identifier and store Personally Identifiable Information.","_rdt_uuid","This cookie is set by Reddit and is used for tracking the views of embedded videos and performance of the advertisements.","AMP_91bf70adfe","Supports Amplitude product analytics.","This cookie name is associated with StackAdapt Inc. which is used to support the effective management and optimization of digital advertising campaigns by handling information such as visitor actions on websites, visited pages, time spent, page load speed, and more.","build.nvidia.com","kndctr_F207D74D549850760A4C98C6_AdobeOrg_cluster","_cs_nnnnnnnnnnnnn","This is a session cookie. This is a pattern type cookie where a random 13-digit number is appended to the prefix _cs_.","_uetsid","This cookie is used by Bing to determine what ads should be shown that may be relevant to the end user perusing the site. ","kndctr_F207D74D549850760A4C98C6_AdobeOrg_bc_session_id","ttcsid_XXXXXXXXXXXXXXXXXXXXCategory","This cookie name is associated with TikTok which is used to track your activity on the platform, including how you interact with their embedded services on other websites.This cookie is associated with TikTok. It helps track your activity on the platform, including how you interact with their embedded services on other websites.","_fbp","Used by Facebook to deliver a series of advertisement products such as real time bidding from third party advertisers","_twpid","This cookie is likely used to track user identity by assigning a unique user ID when the user engages with the website. It is commonly used for analytics and personalization of content.","marketplace.nvidia.com","AMP_MKTG_92dea1e784","This cookie is typically associated with SnackTools, which is a suite of web applications for creating and sharing multimedia content. It is used to identify a user across sessions and track user activities.","forums.developer.nvidia.com","This cookie is typically associated with the use of Taptap Digital, a company specializing in digital advertising. It is used for tracking and ad personalization purposes.","_tt_enable_cookie","This cookie name is associated with TikTok which is used to collect data about behavior and purchases on the website and to measure the effect of advertising. It is also used to track website activity to help optimize advertising efforts.","AMCV_xxxxxAdobeOrg","This cookie is used to identify a unique visitor for tracking purposes by Adobe Experience Cloud.This is a pattern type cookie name associated with Adobe Marketing Cloud. It stores a unique visitor identifier, and uses an organisation identifier to allow a company to track users across their domains and services.","ttcsid","This cookie name is associated with TikTok which is used to enable TikTok Ads session tracking by assigning a unique session ID to users who click on TikTok ads, allowing for the attribution of user behavior and conversions within the same session.This cookie is associated with TikTok. It helps track your activity on the platform, including how you interact with their embedded services on other websites.","AMP_MKTG_91bf70adfe","C0003","Personalization Cookies","These cookies collect data about how you have interacted with our website to help us improve your web experience, such as which pages you have visited. These cookies may store a unique ID so that our system will remember you when you return. They may be set by us or by third party providers whose services we have added to our pages. These cookies enable us to provide enhanced website functionality and personalization as well as make the marketing messages we send to you more relevant to your interests. If you do not allow these cookies, then some or all of these services may not function properly.",4,[615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635],[580,581,582,583,584],{"_381":474,"_91":474,"_90":383,"_354":606},{"_381":440,"_91":440,"_90":383,"_354":601},{"_381":594,"_91":594,"_90":383,"_354":595},{"_381":590,"_91":590,"_90":383,"_354":591},{"_381":585,"_91":585,"_90":383,"_354":586},"nvcrm.my.site.com",[587],{"_232":588,"_388":585,"_389":26,"_90":589},"BrowserId","If you know anything about this cookie and its uses that are not specific to a particular site please add your contributions.","nvidia.partners",[592],{"_232":593,"_388":590,"_389":26,"_90":423},"edge","github.com",[596,597],{"_232":600,"_388":594,"_389":26,"_90":599},{"_232":598,"_388":594,"_389":26,"_90":599},"logged_in","This domain is owned by Github. 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