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Recalibration Error

Tutorials FAQs Presentations Common Problems Methods and Algorithms Dictionary GATK 4 Alpha Pipelining with Queue Developer Zone Archive Tools related to GATK MuTect v1 MuTect v1 Documentation ReCapSeg ReCapSeg Documentation Oncotator Oncotator documentation GenomeSTRiP GenomeSTRiP Documentation XHMM Firepony Base Recalibrator search subcategories search archived Tags What to search discussions questions comments answers groups Date within 1 day 3 days 1 week 2 weeks 1 month 2 months 6 months 1 year of Examples: Monday, today, last week, Mar 26, 3/26/04 Search Howdy, Stranger! It looks like you're new here. If you want to get involved, click one of these buttons! Sign In Register Categories Recent Discussions Activity Best Of... Unanswered Groups Categories 6.5K All Categories186 Announcements 5.6K Ask the GATK team 216 GATK Documentation Guide 30 Tutorials 44 FAQs 12 Presentations 11 Common Problems 32 Methods and Algorithms 18 Dictionary 10 GATK 4 Alpha 1 Pipelining with Queue 30 Developer Zone 28 Archive 455 Tools related to GATK 129 MuTect v1 11 ReCapSeg 36 Oncotator 250 GenomeSTRiP 26 XHMM 3 Firepony Base Recalibrator Powered by Vanilla. Made with Bootstrap. Register now for the upcoming GATK Best Practices workshop, Nov 7-8 at the Broad in Cambridge, MA. Open to all comers! More info and signup at https://goo.gl/forms/mFeERlIeLuJ95Idm1 Indels Recalibration error message rcholic DenverPosts: 68Member ✭ July 2013 in Ask the GATK team I am trying to recalibrate my VCF files for Indels calling using the below command lines: java -Xmx2G -jar ../GenomeAnalysisTK.jar -T VariantRecalibrator \ -R ../GATK_ref/hg19.fasta \ -input ./Variants/gcat_set_053_2.raw.snps.indels.vcf \ -nt 4 \ -resource:mills,known=false,training=true,truth=true,prior=12.0 ../GATK_ref/Mills_and_1000G_gold_standard.indels.hg19.vcf \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ../GATK_ref/dbsnp_137.hg19.vcf \ -an DP -an FS -an ReadPosRankSum -an MQRankSum \ --maxGaussians 4 \ -percentBad 0.05 \ -minNumBad 1000 \ -mode INDEL \ -recalFile ./Variants/VQSR/gcat_set_053_2.indels.vcf.recal \ -tranchesFile ./Variants/VQSR/gcat_set_053_2.indels.tranches \ -rscriptFile ./Variants/VQSR/gcat_set_053_2.indels.recal.plots.R > ./Variants/VQSR/IndelRecal2-noAnnot.log I got this error message, even after taking the recommendation (e.g. maxGaussians 4, --percentBad 0.05). What does this error message mean? my files have too few variants

Επιλέξτε τη γλώσσα σας. Κλείσιμο Μάθετε περισσότερα View this message in English Το YouTube εμφανίζεται στα Ελληνικά. Μπορείτε να αλλάξετε αυτή την προτίμηση παρακάτω. Learn more You're viewing YouTube in Greek. You can change this preference below. Κλείσιμο Ναι, θέλω να τη κρατήσω Αναίρεση Κλείσιμο Αυτό το βίντεο δεν είναι διαθέσιμο. Ουρά παρακολούθησηςΟυράΟυρά παρακολούθησηςΟυρά Κατάργηση όλωνΑποσύνδεση http://gatkforums.broadinstitute.org/gatk/discussion/2967/indels-recalibration-error-message Φόρτωση... Ουρά παρακολούθησης Ουρά __count__/__total__ Recalibration error 2.0 HeyItzMax GAMER ΕγγραφήΕγγραφήκατεΚατάργηση εγγραφής5757 Φόρτωση... Φόρτωση... Σε λειτουργία... Προσθήκη σε... Θέλετε να το δείτε ξανά αργότερα; Συνδεθείτε για να προσθέσετε το βίντεο σε playlist. Σύνδεση Κοινή χρήση https://www.youtube.com/watch?v=1sQGb8zFJVg Περισσότερα Αναφορά Θέλετε να αναφέρετε το βίντεο; Συνδεθείτε για να αναφέρετε ακατάλληλο περιεχόμενο. Σύνδεση 27 προβολές 3 Σας αρέσει αυτό το βίντεο; Συνδεθείτε για να μετρήσει η άποψή σας. Σύνδεση 4 1 Δεν σας αρέσει αυτό το βίντεο; Συνδεθείτε για να μετρήσει η άποψή σας. Σύνδεση 2 Φόρτωση... Φόρτωση... Φόρτωση... Η δυνατότητα αξιολόγησης είναι διαθέσιμη όταν το βίντεο είναι ενοικιασμένο. Αυτή η λειτουργία δεν είναι διαθέσιμη αυτήν τη στιγμή. Δοκιμάστε ξανά αργότερα. Δημοσιεύτηκε στις 19 Φεβ 2016Espero que les guste =) Κατηγορία Πρόσωπα και ιστολόγια Άδεια Τυπική άδεια YouTube Προτείνεται από Dream Crusher Media Bossfight Εμφάνιση περισσότερων Εμφάνιση λιγότερων Φόρτωση... Διαφήμιση Αυτόματη αναπαραγωγ

1 Thread: PCDelta Error after recalibration reverted stat change, took money and increased cost. | Forums Thread Tools Show Printable Version Email this http://forums.ubi.com/showthread.php/1431612-Delta-Error-after-recalibration-reverted-stat-change-took-money-and-increased-cost-Forums Page… Search Thread Advanced Search Display Linear Mode Switch to Hybrid http://seqanswers.com/forums/showthread.php?t=65622 Mode Switch to Threaded Mode 04-12-2016,11:24 PM #1 DuckingCover View Profile View Forum Posts Private Message Junior Member Join Date Nov 2006 Posts 4 Delta Error after recalibration reverted stat change, took money and increased cost. Recalibrated crafted striker's mask at station, chose to roll 8.5 ballistic shield recalibration error health into first aid ally heal. Exited recalibration station. Was disconnected (Delta). Upon reconnection, mask is back to 8.5% ballistic shield health, however, the line is highlighted as if it has been recalibrated, and the cost is now 106k. Boo. I've since rerolled it again, because ballistic shield is terrible, and now it's sticky bomb. I've quit and relaunched, mask recalibration error is still sticky bomb. Atomic transactions would be cool. Reply Reply With Quote Quick Navigation PC Top Site Areas Settings Private Messages Subscriptions Search Forums Forums Home Forums For Honor Japan Alpha 一般的な話題 ゲーム情報 フィードバック 戦闘 マップ モード カスタマイズと成長 キャラクター テクニカルサポート Official News and Announcements General Discussion Suggestions & Feedback Ghost Recon Ghost Recon Wildlands News and Announcements General Discussion Community Content Off-Topic Ghost Recon Future Soldier Ghost Recon: Future Soldier [Console] Ghost Recon: Future Soldier [PC] Ghost Recon Legacy Ghost Recon Legacy [Console] Ghost Recon Legacy [PC] Ghost Recon Team Recruiting Ghost Recon Tech Support - Self Help Steep Steep Steep - News & Announcement Steep - General Discussion South Park News & Announcements South Park: The Fractured But Whole Suggestions & Feedback Technical Support Rainbow Six News & Announcements General Discussion Player Content Off Topic Community Competition Tactics & Strategy Multiplayer Terrorist Hunt Technical Issues PC Console Feedback Maps Operators Game Modes Group Recruitment PC XBox One Playstation 4 Legacy Rainbow Six Titles Rainbow Six Vegas Series Rainbow Six Vegas Series [Console] Rainbow Six Veg

as a guest, which limits your access. Click here to register now, and join the discussion Community Links Members List Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page... Similar Threads Thread Thread Starter Forum Replies Last Post GATK Base Quality Recalibration error unknown_0912 Bioinformatics 1 09-21-2015 05:12 PM mini tutorial: build reference mouse genome and SNP for GATK mediator Bioinformatics 2 04-13-2015 08:47 AM GATK with non-model organism (Help with making SNP VCF file)) newbietonextgen Bioinformatics 7 09-10-2012 07:59 AM Novoalign with GATK recalibration trickytank Genomic Resequencing 10 09-12-2011 07:50 PM GATK unified SNP caller error dakl Bioinformatics 4 11-23-2010 09:27 PM Thread Tools 01-17-2016, 04:14 AM #1 discoveradnan Member Location: Pakistan Join Date: Oct 2015 Posts: 22 Facing error while trying to build SNP recalibration model using GATK Hello everyone, Kindly help me in fixing following error while trying to build SNP recalibration model uing GATK, $ java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Reference/hg19.fa -input raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /Reference/hapmap_3.3.hg19.vcf -resourcemni,known=false,training=true,truth=true,prior=12.0 /Reference/1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /Reference/1000G_phase1.snps.high_confidence.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /Reference/dbsnp_138.hg19.vcf -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile recalibrate_SNP.recal -tranchesFile recalibrate_SNP.tranches -rscriptFile recalibrate_SNP_plots.R ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.5-0-g36282e4): ERROR ERROR This means that one or more arguments or inputs in your command are incorrect. ERROR The error message below tells you what is the problem. ERROR ERROR If the problem is


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