mutect

• [ERROR] token_pon_size_update

  Answered 25 views 7 comments 0 points Most recent by esalinas September 22Ask the FireCloud Team
• What does MuTect output means?

  Answered 1.7K views 13 comments 1 point Most recent by Sheila September 1MuTect v1
• Broad Mutation Calling Best Practice Workflows

  1.8K views 10 comments 0 points Most recent by YingLiu September 1Cancer Genome Analysis
• Somatic Variant Calling with Tumor Samples Only

  Answered 913 views 4 comments 0 points Most recent by Sheila August 18Ask the GATK team
• what's the difference between mutect and GATK-Mutect ?

  Answered 100 views 11 comments 0 points Most recent by shlee August 7Ask the GATK team
• MuTect source now available in GitHub!

  Answered Announcement 8.1K views 36 comments 1 point Most recent by vectorio August 3MuTect v1 Documentation
• What is MutectFC for?

  Answered 26 views 1 comment 0 points Most recent by cbao August 2Ask the FireCloud Team
• COSMIC and dbSNP files for MuTect

  Answered 15K views 58 comments 0 points Most recent by YingLiu August 1Ask the GATK team
• Any way to download hellbender-all-1.0.jar?

  Answered 40 views 2 comments 0 points Most recent by KateN July 31Ask the FireCloud Team
• What is the output of MuTect and how should I interpret it?

  10.1K views 40 comments 1 point Most recent by Geraldine_VdAuwera July 21MuTect v1 Documentation
• java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect

  Answered 488 views 2 comments 0 points Most recent by shlee July 11Ask the GATK team
• How should I select samples for a Panel of Normals for somatic analysis?

  316 views 2 comments 0 points Most recent by Sheila June 22Frequently Asked Questions
• Phasing SNPs and Indels

  Answered 69 views 2 comments 0 points Most recent by Sheila June 8Ask the GATK team
• How MuTect identifies candidate somatic mutations

  2.5K views 1 comment 0 points Most recent by cangfengzhe May 20MuTect v1 Documentation
• GATK best pratices for RNA-seq somatic mutation finding

  Answered 387 views 11 comments 0 points Most recent by shlee May 16Ask the GATK team
• How to run MuTect v1 in Queue?

  Answered 128 views 6 comments 0 points Most recent by Sheila May 10Ask the GATK team
• can Mutect be used to detect somatic variants in healthy individuals?

  Answered 104 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 27MuTect v1
• Mutect is not working

  Answered 1.5K views 10 comments 0 points Most recent by GourabSaha April 5MuTect v1
• AD different with DP

  Answered 123 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 22MuTect v1
• Mutect build Failure

  Answered 48 views 2 comments 0 points Most recent by apchumangenomics March 16Ask the GATK team
• Error I meet when install MuTect on a linux server

  Answered 124 views 4 comments 1 point Most recent by rafi March 14Ask the GATK team
• exome best practice

  Answered 90 views 3 comments 0 points Most recent by Sheila March 7Ask the GATK team
• Allele frequency and depth VCF produced by MuTect2

  Answered 165 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 22Ask the GATK team
• Somatic mutations of epithelial cells (HaplotypeCaller vs Mutect)

  Answered 516 views 2 comments 0 points Most recent by firadazer February 21Ask the GATK team
• Version highlights for GATK version 3.5

  2K views 23 comments 1 point Most recent by shlee February 16Announcements
• Cancer variant calling workflow with mutect and changes/additions to the GATK best practices

  Answered 1.8K views 5 comments 0 points Most recent by Geraldine_VdAuwera January 21MuTect v1
• cryptic invocationTargetException error

  Answered 98 views 1 comment 0 points Most recent by ncamarda November 2016MuTect v1
• mutect wig.txt file

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

  366 views 0 comments 0 points Started by jneff November 2016 Cancer Genome Analysis
• How MuTect filters candidate mutations

  8.1K views 22 comments 0 points Most recent by RikyJKD October 2016MuTect v1 Documentation
• MuTect2 and multiple read groups per sample, issue with index

  Answered 519 views 8 comments 0 points Most recent by Sheila October 2016Ask the GATK team
• Mutect variant calling the parameters for filtering

  Answered 209 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• GATK best practices somatic mutations

  Answered 229 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• Mutect version of Picard tool for filtering

  Answered 69 views 2 comments 0 points Most recent by Sheila September 2016Ask the GATK team
• disable strand bias and clustered position filters, mutect

  Answered 1.2K views 7 comments 0 points Most recent by Eugenie September 2016MuTect v1
• Not all FORMAT fields are being emitted

  Answered 138 views 3 comments 0 points Most recent by Sheila August 2016Ask the GATK team
• Reduce mutect running time

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

  Answered 123 views 1 comment 0 points Most recent by Sheila July 2016MuTect v1
• MuTect with hg38(GRCh38) reference

  Answered 552 views 1 comment 0 points Most recent by shlee July 2016MuTect v1
• Interpret MuTect result

  Answered 181 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 280 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 371 views 1 comment 0 points Most recent by shlee June 2016Ask the GATK team
• fixmisencoded quality scores for combination of correct and incorrect encoding

  Answered 192 views 2 comments 0 points Most recent by Sheila June 2016Ask the GATK team
• MuTect 1.1.6 .jar?

  Answered 268 views 2 comments 0 points Most recent by Geraldine_VdAuwera June 2016MuTect v1
• Running Mutect on paired-end vs. single-end read data

  233 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

  Answered 400 views 1 comment 0 points Most recent by Geraldine_VdAuwera May 2016Ask the GATK team
• MuTect unable to detect some germline mutations

  Answered 241 views 3 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect FA = 0 when variant Pass

  Answered 126 views 2 comments 0 points Most recent by Sheila May 2016MuTect v1
• MuTect is Picking up Germline Mutations that are in dbSNP

  Answered 246 views 2 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect1 strand information

  Answered 228 views 5 comments 0 points Most recent by Geraldine_VdAuwera May 2016MuTect v1
• Read contigs contain both GRch37 and hg19 indices

  Answered 311 views 1 comment 0 points Most recent by Sheila May 2016Ask the GATK team
• Rescuing variants Tumor In Normal Contamination--AF fit

  Answered 266 views 2 comments 0 points Most recent by tbrunetti May 2016MuTect v1
• What input files does MuTect accept / require?

  5.2K views 37 comments 0 points Most recent by weini_huang May 2016MuTect v1 Documentation
• MuTect v2 t_LOD filtering

  Answered 244 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2016Ask the GATK team
• mutect2 release date

  Answered 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 226 views 1 comment 0 points Most recent by Lanting Guo March 2016MuTect v1
• Mutect2 takes too mach time？

  Answered 321 views 1 comment 0 points Most recent by Sheila March 2016Ask the GATK team
• short read preprocessing in MuTect

  Answered 248 views 6 comments 0 points Most recent by jingmeng February 2016Ask the GATK team
• How is "germline_risk" failure reason for MuTect assigned?

  Answered 261 views 2 comments 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Release notes for GATK version 3.5

  1.2K views 7 comments 0 points Most recent by Geraldine_VdAuwera February 2016Announcements
• Mutect output reproducibility?

  Answered 134 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Can I filter with dbsnp/cosmic post mutect?

  Answered 838 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 140 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Germline risk variant calling for cancer WES

  Answered 585 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016Ask the GATK team
• Broad Mini Mutation Calling Workspace

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

  Answered 260 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• Duplicate mutation in oncotator output

  Answered 336 views 2 comments 0 points Most recent by Geraldine_VdAuwera December 2015Oncotator
• MuTect2 output

  Answered 614 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2015Ask the GATK team
• About mutect output

  Answered 155 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

  Answered 794 views 5 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• MuTect quality score

  Answered 856 views 8 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Number of mutated reads different between Mutect and IGV

  Answered 169 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• removing low-quality reads by MuTect

  Answered 230 views 2 comments 0 points Most recent by jingmeng November 2015Ask the GATK team
• Mutect for Rat data

  Answered 172 views 4 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Problems in building mutect from github

  Answered 290 views 2 comments 0 points Most recent by jingmeng November 2015MuTect v1
• What is MuTect?

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

  Answered 574 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 163 views 6 comments 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• a problem about "ExceptionInInitializerError" from running Mutect1.1.7.jar

  Answered 187 views 4 comments 0 points Most recent by xdzperfect October 2015Ask the GATK team
• How mutect treat paired end downsampled reads?

  Answered 289 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• MuTect - No tribble type error

  Answered 417 views 6 comments 0 points Most recent by SebBat October 2015MuTect v1
• Comparison method violates its general contract!

  Answered 974 views 5 comments 0 points Most recent by jlrflores October 2015Ask the GATK team
• How does Mutect "work"?

  Answered 225 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• How to emit only "Keep" or "Covered" calls from MuTect

  Answered 211 views 1 comment 0 points Most recent by Geraldine_VdAuwera September 2015MuTect v1
• What resource data files are needed for running MuTect?

  1.7K 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

  Answered 759 views 15 comments 0 points Most recent by nroak September 2015Ask the GATK team
• Build Error: GATK Framework

  Answered 492 views 4 comments 0 points Most recent by ramanibk September 2015Ask the GATK team
• SomaticSpike

  Answered 190 views 3 comments 0 points Most recent by Sheila September 2015Ask the GATK team
• How does MuTect handles overlapping reads?

  Answered 317 views 4 comments 0 points Most recent by asowalsky August 2015MuTect v1
• Bug reporting for MuTect

  Answered 140 views 2 comments 0 points Most recent by Geraldine_VdAuwera July 2015MuTect v1
• Increase read depth for MuTect?

  Answered 310 views 2 comments 0 points Most recent by ssoderman July 2015MuTect v1
• get germline variants for mutect

  Question 382 views 0 comments 0 points Started by szimmerm June 2015 Ask the GATK team
• MuTect use of mixed

  Question 106 views 0 comments 0 points Started by jorgezajgla June 2015 Ask the GATK team
• Threshold for base phred quality

  Answered 614 views 4 comments 0 points Most recent by epinatel May 2015Ask the GATK team
• MuTect on mitochondrial genome

  Answered 229 views 2 comments 0 points Most recent by ramiro2k May 2015Ask the GATK team
• Allele depth difference between mutect VCF and IGV

  Answered 601 views 3 comments 0 points Most recent by Geraldine_VdAuwera April 2015MuTect v1
• Mutect VCF output

  Answered 2.9K 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 505 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2015MuTect v1
• Mutect with multiple bams or single bams

  Answered 650 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 499 views 4 comments 0 points Most recent by Anatli February 2015MuTect v1