mutect

Discussion List

• Mutect2 version 4.0.11.0 still get empty vcf with one sample for PON,and filter 1000 sites

  Answered 56 views 9 comments 0 points Most recent by manba December 7Ask the GATK team
• Mutect2 troubleshooting

  Accepted Answer 32 views 4 comments 0 points Most recent by igor December 7Ask the GATK team
• Infuence of Coverage Depth Difference in Tumor & Normal Sequencing Data in Somatic Mutation Calling

  Answered 38 views 1 comment 0 points Most recent by AdelaideR December 4Ask the GATK team
• Unable to close output stream with exception Disk quota exceeded error

  Accepted Answer 683 views 3 comments 0 points Most recent by y.song October 13Ask the GATK team
• Non model organisms SNP database

  Question 21 views 0 comments 0 points Started by kmmahan October 8 Ask the GATK team
• MuTect2: Reference name for '3223094' not found in sequence dictionary

  Answered 43 views 6 comments 0 points Most recent by michaelmc September 10Ask the GATK team
• How MuTect identifies candidate somatic mutations

  3.7K views 4 comments 0 points Most recent by dcraig01 August 1MuTect v1 Documentation
• Broad Mutation Calling Best Practice Workflows

  4.1K views 28 comments 0 points Most recent by JohnyWalter July 16Cancer Genome Analysis
• MuTect quality score

  Question 1.1K views 9 comments 0 points Most recent by student-t June 21MuTect v1
• Appropriate WGS Mutect normal_panel

  Accepted Answer 51 views 1 comment 0 points Most recent by Sheila June 20Ask the GATK team
• Calling Somatic Variants without matched normals using GATK.

  Answered 117 views 1 comment 0 points Most recent by Sheila June 7Ask the GATK team
• gatk4: Mutect2 miss real variants

  Accepted Answer 181 views 2 comments 0 points Most recent by mauriziopolano May 15Ask the GATK team
• GATK4 Mutect2 bundle resources

  Accepted Answer 206 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 2.3K views 8 comments 0 points Most recent by Geraldine_VdAuwera February 6MuTect v1
• Positivo control for MUTECT2 evaluate locally

  Accepted Answer 140 views 5 comments 0 points Most recent by mattoslmp January 17Ask the FireCloud Team
• How MuTect filters candidate mutations

  11.4K views 23 comments 0 points Most recent by bioinfolearner December 2017MuTect v1 Documentation
• COSMIC and dbSNP files for MuTect

  Accepted Answer 17.3K views 59 comments 0 points Most recent by iriantoj November 2017Ask the GATK team
• [ERROR] token_pon_size_update

  Accepted Answer 67 views 10 comments 0 points Most recent by cbao September 2017Ask the FireCloud Team
• What does MuTect output means?

  Answered 2.6K views 13 comments 1 point Most recent by Sheila September 2017MuTect v1
• Somatic Variant Calling with Tumor Samples Only

  Accepted Answer 1.6K views 4 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• what's the difference between mutect and GATK-Mutect ?

  Answered 386 views 11 comments 0 points Most recent by shlee August 2017Ask the GATK team
• MuTect source now available in GitHub!

  Answered Announcement 9.1K views 36 comments 1 point Most recent by vectorio August 2017MuTect v1 Documentation
• What is MutectFC for?

  Accepted Answer 48 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 73 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?

  12.7K views 40 comments 1 point Most recent by Geraldine_VdAuwera July 2017MuTect v1 Documentation
• java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect

  Answered 612 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?

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

  Accepted Answer 366 views 2 comments 0 points Most recent by Sheila June 2017Ask the GATK team
• GATK best pratices for RNA-seq somatic mutation finding

  Answered 948 views 11 comments 0 points Most recent by shlee May 2017Ask the GATK team
• How to run MuTect v1 in Queue?

  Accepted Answer 223 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 187 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2017MuTect v1
• Mutect is not working

  Accepted Answer 1.9K views 10 comments 0 points Most recent by GourabSaha April 2017MuTect v1
• AD different with DP

  Accepted Answer 219 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2017MuTect v1
• Mutect build Failure

  Accepted Answer 95 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 245 views 4 comments 1 point Most recent by rafi March 2017Ask the GATK team
• exome best practice

  Answered 146 views 3 comments 0 points Most recent by Sheila March 2017Ask the GATK team
• Allele frequency and depth VCF produced by MuTect2

  Answered 543 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 918 views 2 comments 0 points Most recent by firadazer February 2017Ask the GATK team
• Version highlights for GATK version 3.5

  2.7K views 23 comments 1 point Most recent by shlee February 2017Announcements
• cryptic invocationTargetException error

  Accepted Answer 168 views 1 comment 0 points Most recent by ncamarda November 2016MuTect v1
• mutect wig.txt file

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

  897 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 844 views 8 comments 0 points Most recent by Sheila October 2016Ask the GATK team
• Mutect variant calling the parameters for filtering

  Accepted Answer 395 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• GATK best practices somatic mutations

  Accepted Answer 549 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• Mutect version of Picard tool for filtering

  Answered 107 views 2 comments 0 points Most recent by Sheila September 2016Ask the GATK team
• disable strand bias and clustered position filters, mutect

  Answered 1.4K views 7 comments 0 points Most recent by Eugenie September 2016MuTect v1
• Not all FORMAT fields are being emitted

  Accepted Answer 209 views 3 comments 0 points Most recent by Sheila August 2016Ask the GATK team
• Reduce mutect running time

  857 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 169 views 1 comment 0 points Most recent by Sheila July 2016MuTect v1
• MuTect with hg38(GRCh38) reference

  Accepted Answer 827 views 1 comment 0 points Most recent by shlee July 2016MuTect v1
• Interpret MuTect result

  Accepted Answer 241 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 509 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 308 views 2 comments 0 points Most recent by Sheila June 2016Ask the GATK team
• MuTect 1.1.6 .jar?

  Accepted Answer 469 views 2 comments 0 points Most recent by Geraldine_VdAuwera June 2016MuTect v1
• Running Mutect on paired-end vs. single-end read data

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

  Answered 313 views 3 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect FA = 0 when variant Pass

  Answered 170 views 2 comments 0 points Most recent by Sheila May 2016MuTect v1
• Mutect1 strand information

  Accepted Answer 273 views 5 comments 0 points Most recent by Geraldine_VdAuwera May 2016MuTect v1
• Read contigs contain both GRch37 and hg19 indices

  Accepted Answer 505 views 1 comment 0 points Most recent by Sheila May 2016Ask the GATK team
• Rescuing variants Tumor In Normal Contamination--AF fit

  Accepted Answer 423 views 2 comments 0 points Most recent by tbrunetti May 2016MuTect v1
• What input files does MuTect accept / require?

  6K views 37 comments 0 points Most recent by weini_huang May 2016MuTect v1 Documentation
• MuTect v2 t_LOD filtering

  Accepted Answer 416 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2016Ask the GATK team
• mutect2 release date

  Answered 2.3K views 8 comments 0 points Most recent by Sheila April 2016Ask the GATK team
• refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf

  Answered 297 views 1 comment 0 points Most recent by Lanting Guo March 2016MuTect v1
• Mutect2 takes too mach time？

  Answered 465 views 1 comment 0 points Most recent by Sheila March 2016Ask the GATK team
• short read preprocessing in MuTect

  Answered 319 views 6 comments 0 points Most recent by jingmeng February 2016Ask the GATK team
• How is "germline_risk" failure reason for MuTect assigned?

  Answered 433 views 2 comments 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Release notes for GATK version 3.5

  1.5K views 7 comments 0 points Most recent by Geraldine_VdAuwera February 2016Announcements
• Mutect output reproducibility?

  Answered 161 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Can I filter with dbsnp/cosmic post mutect?

  Answered 1.2K 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 223 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016MuTect v1
• Germline risk variant calling for cancer WES

  Accepted Answer 823 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016Ask the GATK team
• Broad Mini Mutation Calling Workspace

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

  Accepted Answer 359 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• Duplicate mutation in oncotator output

  Answered 460 views 2 comments 0 points Most recent by Geraldine_VdAuwera December 2015Oncotator
• MuTect2 output

  Answered 687 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2015Ask the GATK team
• About mutect output

  Accepted Answer 192 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 1.2K views 5 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Number of mutated reads different between Mutect and IGV

  Answered 203 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• removing low-quality reads by MuTect

  Accepted Answer 312 views 2 comments 0 points Most recent by jingmeng November 2015Ask the GATK team
• Mutect for Rat data

  Accepted Answer 202 views 4 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1
• Problems in building mutect from github

  Accepted Answer 363 views 2 comments 0 points Most recent by jingmeng November 2015MuTect v1
• What is MuTect?

  2.9K views 2 comments 0 points Most recent by Geraldine_VdAuwera November 2015MuTect v1 Documentation
• how to choose the cosmic file for MuTect

  Accepted Answer 727 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 200 views 6 comments 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• a problem about "ExceptionInInitializerError" from running Mutect1.1.7.jar

  Answered 221 views 4 comments 0 points Most recent by xdzperfect October 2015Ask the GATK team
• How mutect treat paired end downsampled reads?

  Answered 354 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015MuTect v1
• MuTect - No tribble type error

  Accepted Answer 555 views 6 comments 0 points Most recent by SebBat October 2015MuTect v1
• 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 288 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 258 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 1.2K views 15 comments 0 points Most recent by nroak September 2015Ask the GATK team
• Build Error: GATK Framework

  Accepted Answer 645 views 4 comments 0 points Most recent by ramanibk September 2015Ask the GATK team
• SomaticSpike

  Answered 247 views 3 comments 0 points Most recent by Sheila September 2015Ask the GATK team
• How does MuTect handles overlapping reads?

  Accepted Answer 379 views 4 comments 0 points Most recent by asowalsky August 2015MuTect v1
• Bug reporting for MuTect

  Answered 194 views 2 comments 0 points Most recent by Geraldine_VdAuwera July 2015MuTect v1
• Increase read depth for MuTect?

  Accepted Answer 397 views 2 comments 0 points Most recent by ssoderman July 2015MuTect v1