mutect

Discussion List

• How MuTect identifies candidate somatic mutations

  3.4K views 4 comments 0 points Most recent by dcraig01 August 1MuTect v1 Documentation
• MuTect quality score

  Question 1K views 9 comments 0 points Most recent by student-t June 21MuTect v1
• Cancer variant calling workflow with mutect and changes/additions to the GATK best practices

  Answered 2.2K views 8 comments 0 points Most recent by Geraldine_VdAuwera February 6MuTect v1
• How MuTect filters candidate mutations

  10.6K views 23 comments 0 points Most recent by bioinfolearner December 2017MuTect v1 Documentation
• COSMIC and dbSNP files for MuTect

  Accepted Answer 16.8K views 59 comments 0 points Most recent by iriantoj November 2017Ask the GATK team
• MuTect source now available in GitHub!

  Answered Announcement 8.9K views 36 comments 1 point Most recent by vectorio August 2017MuTect v1 Documentation
• What is the output of MuTect and how should I interpret it?

  12.1K views 40 comments 1 point Most recent by Geraldine_VdAuwera July 2017MuTect v1 Documentation
• java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect

  Answered 565 views 2 comments 0 points Most recent by shlee July 2017Ask the GATK team
• Mutect is not working

  Accepted Answer 1.9K views 10 comments 0 points Most recent by GourabSaha April 2017MuTect v1
• mutect wig.txt file

  683 views 4 comments 0 points Most recent by jlrflores November 2016MuTect v1
• disable strand bias and clustered position filters, mutect

  Answered 1.4K views 7 comments 0 points Most recent by Eugenie September 2016MuTect v1
• Reduce mutect running time

  819 views 5 comments 0 points Most recent by Lien August 2016MuTect v1
• What input files does MuTect accept / require?

  5.8K views 37 comments 0 points Most recent by weini_huang May 2016MuTect v1 Documentation
• Can I filter with dbsnp/cosmic post mutect?

  Answered 1.1K views 9 comments 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Mutect for Rat data

  Accepted Answer 195 views 4 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• What is MuTect?

  2.7K views 2 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1 Documentation
• Comparison method violates its general contract!

  Answered 1.1K views 5 comments 0 points Most recent by jlrflores October 2015Ask the GATK team
• How does Mutect "work"?

  Answered 277 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• How to emit only "Keep" or "Covered" calls from MuTect

  Accepted Answer 248 views 1 comment 0 points Most recent by Geraldine_VdAuwera September 2015MuTect v1
• What resource data files are needed for running MuTect?

  1.9K views 6 comments 0 points Most recent by Geraldine_VdAuwera September 2015MuTect v1 Documentation
• Badly formed genome loc: Contig 'chr1' does not match any contig in the GATK sequence dictionary

  Accepted Answer 1.1K views 15 comments 0 points Most recent by nroak September 2015Ask the GATK team
• Build Error: GATK Framework

  Accepted Answer 619 views 4 comments 0 points Most recent by ramanibk September 2015Ask the GATK team
• SomaticSpike

  Answered 240 views 3 comments 0 points Most recent by Sheila September 2015Ask the GATK team
• How does MuTect handles overlapping reads?

  Accepted Answer 360 views 4 comments 0 points Most recent by asowalsky August 2015MuTect v1
• Bug reporting for MuTect

  Answered 179 views 2 comments 0 points Most recent by Geraldine_VdAuwera July 2015MuTect v1
• Increase read depth for MuTect?

  Accepted Answer 373 views 2 comments 0 points Most recent by ssoderman July 2015MuTect v1
• get germline variants for mutect

  Question 426 views 0 comments 0 points Started by szimmerm June 2015 Ask the GATK team
• MuTect use of mixed

  Question 118 views 0 comments 0 points Started by jorgezajgla June 2015 Ask the GATK team
• Threshold for base phred quality

  Answered 725 views 4 comments 0 points Most recent by epinatel May 2015Ask the GATK team
• MuTect on mitochondrial genome

  Accepted Answer 270 views 2 comments 0 points Most recent by ramiro2k May 2015Ask the GATK team
• Allele depth difference between mutect VCF and IGV

  Answered 743 views 3 comments 0 points Most recent by Geraldine_VdAuwera April 2015MuTect v1
• Mutect VCF output

  Accepted Answer 3.7K views 5 comments 0 points Most recent by Geraldine_VdAuwera April 2015MuTect v1
• Does MuTect 1.1.4 properly handle reads aligned with bwa mem, with or without '-M'?

  Answered 572 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2015MuTect v1
• Mutect with multiple bams or single bams

  Accepted Answer 723 views 1 comment 0 points Most recent by Geraldine_VdAuwera March 2015MuTect v1
• Should I realign around indels and recalibrate quality score before running Mutect?

  Answered 582 views 4 comments 0 points Most recent by Anatli February 2015MuTect v1
• vcf output question

  Answered 2.3K views 6 comments 0 points Most recent by ealvarez January 2015Ask the GATK team
• Error in interval file for Mutect

  Accepted Answer 207 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2015Ask the GATK team
• Mismatch in chromosome labels in cosmic vs. reference file contigs

  Accepted Answer 812 views 7 comments 0 points Most recent by Geraldine_VdAuwera December 2014Ask the GATK team
• High-depth filter for Mutect calls

  Answered 335 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2014Ask the GATK team
• MuTect cancer specific settings (PON + Tumor LOD)

  Question 627 views 2 comments 0 points Most recent by MrFronk November 2014Ask the GATK team
• Triallelic sites in MuTect

  Answered 686 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2014MuTect v1
• Build a panel of normal for Mutect

  Question 2.6K views 5 comments 0 points Most recent by ste September 2014MuTect v1
• Warning message from Mutect

  Accepted Answer 735 views 6 comments 0 points Most recent by Geraldine_VdAuwera September 2014MuTect v1
• Use TCGA variants instead of COSMIC

  Accepted Answer 678 views 1 comment 0 points Most recent by Geraldine_VdAuwera September 2014Ask the GATK team
• Query regarding passing of VCF files from MuTect to snpEff for annotation

  Accepted Answer 909 views 7 comments 0 points Most recent by vivekdas_1987 September 2014MuTect v1
• Why do I get Reject when it should be Keep

  Answered 171 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 2014Ask the GATK team
• MuTect algorithm

  338 views 4 comments 0 points Most recent by Geraldine_VdAuwera August 2014MuTect v1
• Mutect Analysis without a paired tumour normal & Analysis Criteria

  2.1K views 4 comments 0 points Most recent by vyellapa August 2014MuTect v1
• Mutect Error / warning message

  Accepted Answer 795 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014MuTect v1
• How Can I Get strand Bias Imformation From Mutect?

  Accepted Answer 1.1K views 5 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Mutect Build: Java requirements

  Accepted Answer 745 views 7 comments 0 points Most recent by noushin6 June 2014MuTect v1
• What genome builds does MuTect support?

  934 views 0 comments 0 points Started by Geraldine_VdAuwera May 2014 MuTect v1 Documentation
• What are the platform requirements and software dependencies for running MuTect?

  1K views 0 comments 0 points Started by Geraldine_VdAuwera May 2014 MuTect v1 Documentation
• MuTect with RADseq data - disabling strand bias and clustered position filters

  Question 302 views 0 comments 0 points Started by Liz10683 May 2014 Ask the GATK team
• MuTect support for indel calling?

  Answered 1.8K views 1 comment 0 points Most recent by JiantaoShi February 2014MuTect v1
• Using MuTect with human_g1k_v37

  Accepted Answer 396 views 1 comment 0 points Most recent by JiantaoShi February 2014Ask the GATK team
• Mutect installation

  Question 567 views 0 comments 0 points Started by sebastian_d February 2014 Ask the GATK team
• Error Cumulative probability function returned NaN for argument 0.975 p = 0.975 running MuTect

  579 views 8 comments 0 points Most recent by ygong February 2014Ask the GATK team
• Mutect : Change default MuTect Tumour-normal read cutoff values

  Answered 700 views 1 comment 0 points Most recent by rnahar January 2014Ask the GATK team
• differences between 3 versions of MuTect

  Question 246 views 0 comments 0 points Started by ars51 December 2013 Ask the GATK team
• Mutect - no variants found after chromosome 5

  Question 165 views 0 comments 0 points Started by snowinski December 2013 Ask the GATK team
• Quality Trimming and Mutect

  Question 205 views 0 comments 0 points Started by jackb November 2013 Ask the GATK team
• MuTect t_ref_count vs. assembled genome count

  Answered 258 views 1 comment 0 points Most recent by kcibul November 2013MuTect v1
• extra columns in output

  Question 126 views 0 comments 0 points Started by jlrflores November 2013 Ask the GATK team
• MuTect Build Error using Ant

  Question 438 views 1 comment 0 points Most recent by donfreed November 2013Ask the GATK team
• COSMIC parameter for mouse samples

  Question 249 views 0 comments 0 points Started by igor October 2013 Ask the GATK team
• Welcome to the MuTect Support Forum

  Answered 1.5K views 4 comments 0 points Most recent by rgfowler October 2013MuTect v1
• specifying the intervals

  Answered 729 views 2 comments 0 points Most recent by CrossLaycci October 2013Ask the GATK team
• Appistry webinar on analyzing and annotating cancer genomes

  140 views 0 comments 0 points Started by Geraldine_VdAuwera October 2013 Announcements
• How to get the LOD score for normal samples only

  Question 508 views 0 comments 0 points Started by jiaoshuo September 2013 Ask the GATK team
• what's the meanning?

  550 views 2 comments 0 points Most recent by myshowlo September 2013Ask the GATK team
• what‘s the matter?

  411 views 2 comments 0 points Most recent by myshowlo September 2013Ask the GATK team
• when i run the mutect ,i have a matter.

  336 views 2 comments 0 points Most recent by Geraldine_VdAuwera September 2013Ask the GATK team
• mutect sensitivity

  Question 258 views 0 comments 0 points Started by jlrflores September 2013 Ask the GATK team
• Interpreting the MuTect output context column

  Accepted Answer 786 views 1 comment 0 points Most recent by kcibul September 2013Ask the GATK team
• what can i do？

  Accepted Answer 236 views 8 comments 0 points Most recent by myshowlo August 2013Ask the GATK team
• How can I get information about variant allele frequency?

  Answered 1.5K views 1 comment 0 points Most recent by vyellapa August 2013Ask the GATK team
• MuTect repeatedly hangs

  Accepted Answer 565 views 2 comments 0 points Most recent by Jeremy37 August 2013MuTect v1
• Appistry webinar on using GATK + MuTect for somatic mutations

  497 views 0 comments 0 points Started by Geraldine_VdAuwera July 2013 Announcements
• Proximal gap as read preprocessing filter instead of rejection criteria

  Question 198 views 0 comments 0 points Started by jgould June 2013 Ask the GATK team
• Could MuTect be suitably applied on ChIP-seq data?

  Accepted Answer 409 views 1 comment 0 points Most recent by kcibul June 2013Ask the GATK team
• problem in mutect parallel processing

  Answered 818 views 1 comment 0 points Most recent by gpleo June 2013Ask the GATK team
• Does MuTect work with reduced bam files produced by Reduce Reads?

  Answered 419 views 1 comment 1 point Most recent by kcibul June 2013Ask the GATK team
• Bug report: java.lang.IllegalArgumentException: Comparison method violates its general contract!

  Accepted Answer 6K views 3 comments 0 points Most recent by kcibul April 2013Ask the GATK team
• somatic mutation site REJECT only because of "DBSNP Site"

  Question 1.2K views 1 comment 0 points Most recent by circlez April 2013Ask the GATK team
• dbsnp vcf file error

  Question 398 views 0 comments 0 points Started by moonhj April 2013 Ask the GATK team
• About running options and parsing output file.

  Answered 1.4K views 4 comments 0 points Most recent by kcibul April 2013Ask the GATK team
• No_et and proxy errors

  Accepted Answer 796 views 6 comments 0 points Most recent by jellul March 2013Ask the GATK team
• hg19_cosmic_v54_120711.vcf

  Answered 2.4K views 1 comment 0 points Most recent by kcibul February 2013Ask the GATK team
• How to download MuTect?

  Answered 2.6K views 2 comments 0 points Most recent by Yujian February 2013MuTect v1
• IllegalArgumentException while executing MuTect

  Answered 705 views 1 comment 0 points Most recent by kcibul February 2013MuTect v1
• MuTect has been published and is now freely available!

  Announcement 3.1K views 0 comments 2 points Started by kcibul February 2013 MuTect v1 Documentation
• Filtering out "noisy reads"?

  Accepted Answer 527 views 2 comments 0 points Most recent by jstjohn December 2012Ask the GATK team
• Obtain a copy?

  Answered 246 views 1 comment 0 points Most recent by kcibul December 2012Ask the GATK team
• Filtering "noisy" reads

  Accepted Answer 165 views 2 comments 0 points Most recent by jstjohn November 2012Ask the GATK team
• Preferred Java(JRE) version to be used for MuTect

  Accepted Answer 644 views 2 comments 0 points Most recent by vaibhavvsk August 2012Ask the GATK team