mutect

Discussion List

• Broad Mutation Calling Best Practice Workflows

  2.8K views 27 comments 0 points Most recent by MattB March 21Cancer Genome Analysis
• GATK4 Mutect2 bundle resources

  Answered 45 views 1 comment 0 points Most recent by shlee March 19Ask the GATK team
• Cancer variant calling workflow with mutect and changes/additions to the GATK best practices

  Answered 2.1K views 8 comments 0 points Most recent by Geraldine_VdAuwera February 6MuTect v1
• Positivo control for MUTECT2 evaluate locally

  Accepted Answer 108 views 5 comments 0 points Most recent by mattoslmp January 17Ask the FireCloud Team
• How MuTect filters candidate mutations

  9.8K views 23 comments 0 points Most recent by bioinfolearner December 2017MuTect v1 Documentation
• COSMIC and dbSNP files for MuTect

  Accepted Answer 16.3K views 59 comments 0 points Most recent by iriantoj November 2017Ask the GATK team
• [ERROR] token_pon_size_update

  Accepted Answer 43 views 10 comments 0 points Most recent by cbao September 2017Ask the FireCloud Team
• What does MuTect output means?

  Answered 2.2K views 13 comments 1 point Most recent by Sheila September 2017MuTect v1
• Somatic Variant Calling with Tumor Samples Only

  Accepted Answer 1.2K views 4 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• what's the difference between mutect and GATK-Mutect ?

  Answered 236 views 11 comments 0 points Most recent by shlee August 2017Ask the GATK team
• MuTect source now available in GitHub!

  Answered Announcement 8.7K views 36 comments 1 point Most recent by vectorio August 2017MuTect v1 Documentation
• What is MutectFC for?

  Accepted Answer 35 views 1 comment 0 points Most recent by cbao August 2017Ask the FireCloud Team
• Any way to download hellbender-all-1.0.jar?

  Accepted Answer 56 views 2 comments 0 points Most recent by KateN July 2017Ask the FireCloud Team
• What is the output of MuTect and how should I interpret it?

  11.6K views 40 comments 1 point Most recent by Geraldine_VdAuwera July 2017MuTect v1 Documentation
• java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect

  Answered 529 views 2 comments 0 points Most recent by shlee July 2017Ask the GATK team
• How should I select samples for a Panel of Normals for somatic analysis?

  486 views 2 comments 0 points Most recent by Sheila June 2017Frequently Asked Questions
• Phasing SNPs and Indels

  Accepted Answer 209 views 2 comments 0 points Most recent by Sheila June 2017Ask the GATK team
• How MuTect identifies candidate somatic mutations

  3K views 1 comment 0 points Most recent by cangfengzhe May 2017MuTect v1 Documentation
• GATK best pratices for RNA-seq somatic mutation finding

  Answered 689 views 11 comments 0 points Most recent by shlee May 2017Ask the GATK team
• How to run MuTect v1 in Queue?

  Accepted Answer 177 views 6 comments 0 points Most recent by Sheila May 2017Ask the GATK team
• can Mutect be used to detect somatic variants in healthy individuals?

  Accepted Answer 157 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2017MuTect v1
• Mutect is not working

  Accepted Answer 1.8K views 10 comments 0 points Most recent by GourabSaha April 2017MuTect v1
• AD different with DP

  Accepted Answer 182 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2017MuTect v1
• Mutect build Failure

  Accepted Answer 67 views 2 comments 0 points Most recent by apchumangenomics March 2017Ask the GATK team
• Error I meet when install MuTect on a linux server

  Answered 175 views 4 comments 1 point Most recent by rafi March 2017Ask the GATK team
• exome best practice

  Answered 113 views 3 comments 0 points Most recent by Sheila March 2017Ask the GATK team
• Allele frequency and depth VCF produced by MuTect2

  Answered 296 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2017Ask the GATK team
• Somatic mutations of epithelial cells (HaplotypeCaller vs Mutect)

  Accepted Answer 754 views 2 comments 0 points Most recent by firadazer February 2017Ask the GATK team
• Version highlights for GATK version 3.5

  2.4K views 23 comments 1 point Most recent by shlee February 2017Announcements
• cryptic invocationTargetException error

  Accepted Answer 129 views 1 comment 0 points Most recent by ncamarda November 2016MuTect v1
• mutect wig.txt file

  635 views 4 comments 0 points Most recent by jlrflores November 2016MuTect v1
• Best Practice workflows for Cancer Genome Analysis

  699 views 0 comments 0 points Started by jneff November 2016 Cancer Genome Analysis
• MuTect2 and multiple read groups per sample, issue with index

  Accepted Answer 681 views 8 comments 0 points Most recent by Sheila October 2016Ask the GATK team
• Mutect variant calling the parameters for filtering

  Accepted Answer 298 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• GATK best practices somatic mutations

  Accepted Answer 371 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• Mutect version of Picard tool for filtering

  Answered 82 views 2 comments 0 points Most recent by Sheila September 2016Ask the GATK team
• disable strand bias and clustered position filters, mutect

  Answered 1.3K views 7 comments 0 points Most recent by Eugenie September 2016MuTect v1
• Not all FORMAT fields are being emitted

  Accepted Answer 167 views 3 comments 0 points Most recent by Sheila August 2016Ask the GATK team
• Reduce mutect running time

  782 views 5 comments 0 points Most recent by Lien August 2016MuTect v1
• Parameter "--fraction_contamination" does not work in Mutect-1.1.7

  Accepted Answer 141 views 1 comment 0 points Most recent by Sheila July 2016MuTect v1
• MuTect with hg38(GRCh38) reference

  Accepted Answer 686 views 1 comment 0 points Most recent by shlee July 2016MuTect v1
• Interpret MuTect result

  Accepted Answer 210 views 3 comments 0 points Most recent by shlee July 2016Ask the GATK team
• MuTect --- with more stringent parameter settings I got more mutations -- Is this possible

  Answered 373 views 2 comments 0 points Most recent by Geraldine_VdAuwera June 2016MuTect v1
• Is dbSNP GRCh38.p2.vcf and GRCh38.p7.fa compatible in MuTect??

  Answered 431 views 1 comment 0 points Most recent by shlee June 2016Ask the GATK team
• fixmisencoded quality scores for combination of correct and incorrect encoding

  Accepted Answer 247 views 2 comments 0 points Most recent by Sheila June 2016Ask the GATK team
• MuTect 1.1.6 .jar?

  Accepted Answer 346 views 2 comments 0 points Most recent by Geraldine_VdAuwera June 2016MuTect v1
• Running Mutect on paired-end vs. single-end read data

  260 views 9 comments 0 points Most recent by max_shpak June 2016Ask the GATK team
• Unable to close output stream with exception Disk quota exceeded error

  Accepted Answer 535 views 1 comment 0 points Most recent by Geraldine_VdAuwera May 2016Ask the GATK team
• MuTect unable to detect some germline mutations

  Answered 274 views 3 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect FA = 0 when variant Pass

  Answered 146 views 2 comments 0 points Most recent by Sheila May 2016MuTect v1
• MuTect is Picking up Germline Mutations that are in dbSNP

  Answered 323 views 2 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect1 strand information

  Accepted Answer 251 views 5 comments 0 points Most recent by Geraldine_VdAuwera May 2016MuTect v1
• Read contigs contain both GRch37 and hg19 indices

  Accepted Answer 411 views 1 comment 0 points Most recent by Sheila May 2016Ask the GATK team
• Rescuing variants Tumor In Normal Contamination--AF fit

  Accepted Answer 357 views 2 comments 0 points Most recent by tbrunetti May 2016MuTect v1
• What input files does MuTect accept / require?

  5.6K views 37 comments 0 points Most recent by weini_huang May 2016MuTect v1 Documentation
• MuTect v2 t_LOD filtering

  Accepted Answer 304 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2016Ask the GATK team
• mutect2 release date

  Answered 2.2K views 8 comments 0 points Most recent by Sheila April 2016Ask the GATK team
• refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf

  Answered 255 views 1 comment 0 points Most recent by Lanting Guo March 2016MuTect v1
• Mutect2 takes too mach time？

  Answered 381 views 1 comment 0 points Most recent by Sheila March 2016Ask the GATK team
• short read preprocessing in MuTect

  Answered 281 views 6 comments 0 points Most recent by jingmeng February 2016Ask the GATK team
• How is "germline_risk" failure reason for MuTect assigned?

  Answered 350 views 2 comments 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Release notes for GATK version 3.5

  1.4K views 7 comments 0 points Most recent by Geraldine_VdAuwera February 2016Announcements
• Mutect output reproducibility?

  Answered 142 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Can I filter with dbsnp/cosmic post mutect?

  Answered 1K views 9 comments 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Why do Mutect 1.1.4 Revision: 48042(Latest Version) gives## muTector v1.0.47986 as header?

  Answered 179 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Germline risk variant calling for cancer WES

  Accepted Answer 698 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016Ask the GATK team
• Broad Mini Mutation Calling Workspace

  675 views 0 comments 0 points Started by jneff January 2016 Cancer Genome Analysis
• MuTect Genotype Field

  Accepted Answer 303 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• Duplicate mutation in oncotator output

  Answered 389 views 2 comments 0 points Most recent by Geraldine_VdAuwera December 2015Oncotator
• MuTect2 output

  Answered 651 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2015Ask the GATK team
• About mutect output

  Accepted Answer 172 views 3 comments 0 points Most recent by Geraldine_VdAuwera November 2015Ask the GATK team
• Mutect and 'Lexicographically sorted human genome sequence detected in cosmic' error

  Accepted Answer 1K views 5 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• MuTect quality score

  Answered 967 views 8 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Number of mutated reads different between Mutect and IGV

  Answered 182 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• removing low-quality reads by MuTect

  Accepted Answer 273 views 2 comments 0 points Most recent by jingmeng November 2015Ask the GATK team
• Mutect for Rat data

  Accepted Answer 182 views 4 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Problems in building mutect from github

  Accepted Answer 321 views 2 comments 0 points Most recent by jingmeng November 2015MuTect v1
• What is MuTect?

  2.5K views 2 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1 Documentation
• how to choose the cosmic file for MuTect

  Accepted Answer 657 views 2 comments 0 points Most recent by jingmeng November 2015MuTect v1
• VariantFiltration applied to mutect calls generates substantially different FA in some cases?

  Answered 181 views 6 comments 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• a problem about "ExceptionInInitializerError" from running Mutect1.1.7.jar

  Answered 200 views 4 comments 0 points Most recent by xdzperfect October 2015Ask the GATK team
• How mutect treat paired end downsampled reads?

  Answered 321 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• MuTect - No tribble type error

  Accepted Answer 478 views 6 comments 0 points Most recent by SebBat October 2015MuTect v1
• Comparison method violates its general contract!

  Answered 1K views 5 comments 0 points Most recent by jlrflores October 2015Ask the GATK team
• How does Mutect "work"?

  Answered 257 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 234 views 1 comment 0 points Most recent by Geraldine_VdAuwera September 2015MuTect v1
• What resource data files are needed for running MuTect?

  1.8K 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 963 views 15 comments 0 points Most recent by nroak September 2015Ask the GATK team
• Build Error: GATK Framework

  Accepted Answer 572 views 4 comments 0 points Most recent by ramanibk September 2015Ask the GATK team
• SomaticSpike

  Answered 226 views 3 comments 0 points Most recent by Sheila September 2015Ask the GATK team
• How does MuTect handles overlapping reads?

  Accepted Answer 343 views 4 comments 0 points Most recent by asowalsky August 2015MuTect v1
• Bug reporting for MuTect

  Answered 162 views 2 comments 0 points Most recent by Geraldine_VdAuwera July 2015MuTect v1
• Increase read depth for MuTect?

  Accepted Answer 346 views 2 comments 0 points Most recent by ssoderman July 2015MuTect v1
• get germline variants for mutect

  Question 415 views 0 comments 0 points Started by szimmerm June 2015 Ask the GATK team
• MuTect use of mixed

  Question 113 views 0 comments 0 points Started by jorgezajgla June 2015 Ask the GATK team
• Threshold for base phred quality

  Answered 683 views 4 comments 0 points Most recent by epinatel May 2015Ask the GATK team
• MuTect on mitochondrial genome

  Accepted Answer 252 views 2 comments 0 points Most recent by ramiro2k May 2015Ask the GATK team
• Allele depth difference between mutect VCF and IGV

  Answered 691 views 3 comments 0 points Most recent by Geraldine_VdAuwera April 2015MuTect v1
• Mutect VCF output

  Accepted Answer 3.5K 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 546 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2015MuTect v1