mutect

Discussion List

• Request for Golden standard Somatic mutation datasets

  Answered 35 views 1 comment 0 points Most recent by bhanuGandham November 2019Ask the GATK team
• Mutect2 in GATK 4.1.4 not producing stats file?

  Answered 145 views 2 comments 0 points Most recent by bhanuGandham November 2019Ask the GATK team
• GATK4 Mutect2 bundle resources

  Accepted Answer 978 views 3 comments 0 points Most recent by bhanuGandham October 2019Ask the GATK team
• Alternative resources for Mutect2/GetPileupSummaries when dealing with genome data

  Answered 79 views 3 comments 0 points Most recent by akovalsk September 2019Ask the GATK team
• Mutect Analysis without a paired tumour normal & Analysis Criteria

  2.5K views 5 comments 0 points Most recent by LaboBernard July 2019MuTect v1
• [GATK 4.1.2.0] how OPTIMAL_F_SCORE is calculated in FilterMutectCalls

  Answered 137 views 2 comments 0 points Most recent by davidben April 2019Ask the GATK team
• Getting specific information from Mutect or Mutect2 output

  Answered 36 views 1 comment 0 points Most recent by bhanuGandham April 2019Ask the GATK team
• What does MuTect output means?

  Answered 3.5K views 14 comments 1 point Most recent by fi1d18 April 2019MuTect v1
• How MuTect filters candidate mutations

  13.5K views 24 comments 0 points Most recent by Pau April 2019MuTect v1 Documentation
• Calling Somatic Variants without matched normals using GATK.

  Answered 1K views 4 comments 0 points Most recent by davidben March 2019Ask the GATK team
• large drop in variants in GATK 4.1.0.0 Mutect2

  Accepted Answer 61 views 4 comments 0 points Most recent by bshifaw March 2019Ask the GATK team
• Mutect2 allele specific stats for Multiallelic sites

  Answered 91 views 2 comments 0 points Most recent by bhanuGandham March 2019Ask the GATK team
• Question: Mutect v1 doesnt finds second alternative allele

  Answered 38 views 2 comments 0 points Most recent by bhanuGandham March 2019Ask the GATK team
• Understanding the math behind MUTECT LOD scores

  Answered 238 views 1 comment 0 points Most recent by davidben March 2019Ask the GATK team
• Mutect on mm10

  Answered 113 views 2 comments 0 points Most recent by SChaluvadi January 2019Ask the FireCloud Team
• How Can I Get strand Bias Imformation From Mutect?

  Accepted Answer 1.4K views 9 comments 0 points Most recent by AdelaideR January 2019Ask the GATK team
• Mutect 1 vs Mutect 2

  Accepted Answer 89 views 5 comments 0 points Most recent by kirankumar January 2019Ask the FireCloud Team
• Mutect2 troubleshooting

  Accepted Answer 48 views 4 comments 0 points Most recent by igor December 2018Ask the GATK team
• Mutect2 version 4.0.11.0 still get empty vcf with one sample for PON,and filter 1000 sites

  Answered 161 views 5 comments 0 points Most recent by bhanuGandham December 2018Ask the GATK team
• Infuence of Coverage Depth Difference in Tumor & Normal Sequencing Data in Somatic Mutation Calling

  Answered 216 views 1 comment 0 points Most recent by AdelaideR December 2018Ask the GATK team
• Unable to close output stream with exception Disk quota exceeded error

  Accepted Answer 935 views 3 comments 0 points Most recent by y.song October 2018Ask the GATK team
• Non model organisms SNP database

  Accepted Answer 80 views 0 comments 0 points Started by kmmahan October 2018 Ask the GATK team
• MuTect2: Reference name for '3223094' not found in sequence dictionary

  Answered 239 views 6 comments 0 points Most recent by michaelmc September 2018Ask the GATK team
• How MuTect identifies candidate somatic mutations

  4.5K views 4 comments 0 points Most recent by dcraig01 August 2018MuTect v1 Documentation
• MuTect quality score

  Answered 1.3K views 9 comments 0 points Most recent by student-t June 2018MuTect v1
• Appropriate WGS Mutect normal_panel

  Accepted Answer 158 views 1 comment 0 points Most recent by Sheila June 2018Ask the GATK team
• gatk4: Mutect2 miss real variants

  Accepted Answer 421 views 2 comments 0 points Most recent by mauriziopolano May 2018Ask the GATK team
• Cancer variant calling workflow with mutect and changes/additions to the GATK best practices

  Answered 2.5K views 8 comments 0 points Most recent by Geraldine_VdAuwera February 2018MuTect v1
• Positivo control for MUTECT2 evaluate locally

  Accepted Answer 162 views 5 comments 0 points Most recent by mattoslmp January 2018Ask the FireCloud Team
• COSMIC and dbSNP files for MuTect

  Accepted Answer 18.8K views 59 comments 0 points Most recent by iriantoj November 2017Ask the GATK team
• [ERROR] token_pon_size_update

  Accepted Answer 98 views 10 comments 0 points Most recent by cbao September 2017Ask the FireCloud Team
• Somatic Variant Calling with Tumor Samples Only

  Accepted Answer 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 559 views 11 comments 0 points Most recent by shlee August 2017Ask the GATK team
• MuTect source now available in GitHub!

  Answered Announcement 9.9K views 36 comments 1 point Most recent by vectorio August 2017MuTect v1 Documentation
• What is MutectFC for?

  Accepted Answer 67 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 94 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?

  14.6K views 40 comments 1 point Most recent by Geraldine_VdAuwera July 2017MuTect v1 Documentation
• java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect

  Answered 706 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?

  1K views 2 comments 0 points Most recent by Sheila June 2017Frequently Asked Questions
• Phasing SNPs and Indels

  Accepted Answer 550 views 2 comments 0 points Most recent by Sheila June 2017Ask the GATK team
• GATK best pratices for RNA-seq somatic mutation finding

  Answered 1.4K views 11 comments 0 points Most recent by shlee May 2017Ask the GATK team
• How to run MuTect v1 in Queue?

  Accepted Answer 279 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 208 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2017MuTect v1
• Mutect is not working

  Accepted Answer 2.1K views 10 comments 0 points Most recent by GourabSaha April 2017MuTect v1
• AD different with DP

  Accepted Answer 348 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2017MuTect v1
• Mutect build Failure

  Accepted Answer 143 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 334 views 4 comments 1 point Most recent by rafi March 2017Ask the GATK team
• exome best practice

  Answered 194 views 3 comments 0 points Most recent by Sheila March 2017Ask the GATK team
• Allele frequency and depth VCF produced by MuTect2

  Answered 914 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 1.1K views 2 comments 0 points Most recent by firadazer February 2017Ask the GATK team
• Version highlights for GATK version 3.5

  3K views 23 comments 1 point Most recent by shlee February 2017Announcements
• cryptic invocationTargetException error

  Accepted Answer 219 views 1 comment 0 points Most recent by ncamarda November 2016MuTect v1
• mutect wig.txt file

  832 views 4 comments 0 points Most recent by jlrflores November 2016MuTect v1
• MuTect2 and multiple read groups per sample, issue with index

  Accepted Answer 1K views 8 comments 0 points Most recent by Sheila October 2016Ask the GATK team
• Mutect variant calling the parameters for filtering

  Accepted Answer 518 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• GATK best practices somatic mutations

  Accepted Answer 626 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• Mutect version of Picard tool for filtering

  Answered 143 views 2 comments 0 points Most recent by Sheila September 2016Ask the GATK team
• disable strand bias and clustered position filters, mutect

  Answered 1.6K views 7 comments 0 points Most recent by Eugenie September 2016MuTect v1
• Not all FORMAT fields are being emitted

  Accepted Answer 314 views 3 comments 0 points Most recent by Sheila August 2016Ask the GATK team
• Reduce mutect running time

  1.1K 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 200 views 1 comment 0 points Most recent by Sheila July 2016MuTect v1
• MuTect with hg38(GRCh38) reference

  Accepted Answer 1.1K views 1 comment 0 points Most recent by shlee July 2016MuTect v1
• Interpret MuTect result

  Accepted Answer 276 views 3 comments 0 points Most recent by shlee July 2016Ask the GATK team
• Is dbSNP GRCh38.p2.vcf and GRCh38.p7.fa compatible in MuTect??

  Answered 609 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 427 views 2 comments 0 points Most recent by Sheila June 2016Ask the GATK team
• MuTect 1.1.6 .jar?

  Accepted Answer 734 views 2 comments 0 points Most recent by Geraldine_VdAuwera June 2016MuTect v1
• Running Mutect on paired-end vs. single-end read data

  407 views 9 comments 0 points Most recent by max_shpak June 2016Ask the GATK team
• MuTect unable to detect some germline mutations

  Answered 361 views 3 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect FA = 0 when variant Pass

  Answered 208 views 2 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect1 strand information

  Accepted Answer 303 views 5 comments 0 points Most recent by Geraldine_VdAuwera May 2016MuTect v1
• Read contigs contain both GRch37 and hg19 indices

  Accepted Answer 630 views 1 comment 0 points Most recent by Sheila May 2016Ask the GATK team
• Rescuing variants Tumor In Normal Contamination--AF fit

  Accepted Answer 506 views 2 comments 0 points Most recent by tbrunetti May 2016MuTect v1
• What input files does MuTect accept / require?

  6.5K views 37 comments 0 points Most recent by weini_huang May 2016MuTect v1 Documentation
• MuTect v2 t_LOD filtering

  Accepted Answer 599 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2016Ask the GATK team
• mutect2 release date

  Answered 2.4K views 8 comments 0 points Most recent by Sheila April 2016Ask the GATK team
• refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf

  Answered 367 views 1 comment 0 points Most recent by Lanting Guo March 2016MuTect v1
• Mutect2 takes too mach time？

  Answered 685 views 1 comment 0 points Most recent by Sheila March 2016Ask the GATK team
• short read preprocessing in MuTect

  Answered 368 views 6 comments 0 points Most recent by jingmeng February 2016Ask the GATK team
• How is "germline_risk" failure reason for MuTect assigned?

  Answered 526 views 2 comments 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Release notes for GATK version 3.5

  1.6K views 7 comments 0 points Most recent by Geraldine_VdAuwera February 2016Announcements
• Mutect output reproducibility?

  Answered 182 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Can I filter with dbsnp/cosmic post mutect?

  Answered 1.4K 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?

  Accepted Answer 298 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Germline risk variant calling for cancer WES

  Accepted Answer 994 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016Ask the GATK team
• Broad Mini Mutation Calling Workspace

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

  Accepted Answer 456 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• Duplicate mutation in oncotator output

  Answered 569 views 2 comments 0 points Most recent by Geraldine_VdAuwera December 2015Oncotator
• MuTect2 output

  Answered 764 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2015Ask the GATK team
• About mutect output

  Accepted Answer 221 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 1.5K views 5 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Number of mutated reads different between Mutect and IGV

  Answered 246 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• removing low-quality reads by MuTect

  Accepted Answer 361 views 2 comments 0 points Most recent by jingmeng November 2015Ask the GATK team
• Mutect for Rat data

  Accepted Answer 230 views 4 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Problems in building mutect from github

  Accepted Answer 447 views 2 comments 0 points Most recent by jingmeng November 2015MuTect v1
• What is MuTect?

  3.4K views 2 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1 Documentation
• how to choose the cosmic file for MuTect

  Accepted Answer 890 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 241 views 6 comments 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• a problem about "ExceptionInInitializerError" from running Mutect1.1.7.jar

  Answered 262 views 4 comments 0 points Most recent by xdzperfect October 2015Ask the GATK team
• How mutect treat paired end downsampled reads?

  Answered 431 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1