commandlinegatk

Discussion List

• user error message for HaplotypeCaller in GVCF mode

  Answered 19 views 1 comment 0 points Most recent by rebeccarose January 4Ask the GATK team
• VariantRecalibrator - Can't do comparison because Locatables' contigs not found in sequence dict

  Answered 55 views 4 comments 0 points Most recent by AdelaideR November 2018Ask the GATK team
• Reference Genome ERROR

  Answered 101 views 2 comments 0 points Most recent by fmlad October 2018Ask the Cromwell + WDL Team
• Variant calling: Bam file is indexed but GATK thinks it is not

  Answered 38 views 1 comment 0 points Most recent by bhanuGandham October 2018Ask the GATK team
• RNA-Seq Variant Calling in Antibody Strain

  Answered 33 views 1 comment 0 points Most recent by Sheila April 2018Ask the GATK team
• Problem in a task with piped command

  Accepted Answer 97 views 2 comments 0 points Most recent by NawarDalila March 2018Ask the Cromwell + WDL Team
• QD Annotation error in GATK in VariantRecalibration step

  Answered 50 views 5 comments 0 points Most recent by Sheila March 2018Ask the GATK team
• SortSam in GATK4.0.1 fails, Picard 2.11 SortSam works on the same file

  Accepted Answer 107 views 1 comment 0 points Most recent by NGSman February 2018Ask the GATK team
• define java to use in GATK4?

  Answered 315 views 7 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• Inconsistency between Alt Variant in BAM and bamout from MuTect2

  Answered 52 views 3 comments 0 points Most recent by dsmarcoantonio January 2018Ask the GATK team
• Haplotype Caller Makes SNPs look like INDELS

  Answered 79 views 4 comments 0 points Most recent by Sheila September 2017Ask the GATK team
• VariantRecalibrator for bacterial genome annotation

  Answered 110 views 1 comment 0 points Most recent by Sheila August 2017Ask the GATK team
• Where can I find additional documentation for gatk-queue

  Answered 118 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2017Ask the GATK team
• Removing * Alleles

  Answered 142 views 1 comment 0 points Most recent by Geraldine_VdAuwera June 2017Ask the GATK team
• Parameters in workflow input json not being passed to workflow WDL?

  Accepted Answer 172 views 4 comments 0 points Most recent by [email protected] April 2017Ask the Cromwell + WDL Team
• Joint genotyping using GenotypeGVCFs command line

  Answered 881 views 3 comments 0 points Most recent by Sheila February 2017Ask the GATK team
• Known sites for indel realignment and BQSR in hg38 bundle

  Accepted Answer 1.8K views 4 comments 0 points Most recent by Sheila February 2017Ask the GATK team
• GATK3.7 GenotypeGVCFs Runtime Error

  440 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2016Ask the GATK team
• How to get output in java script

  Accepted Answer 107 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2016Ask the GATK team
• Specify number of cores for each task in LSF

  Accepted Answer 381 views 1 comment 0 points Most recent by kshakir November 2016Ask the Cromwell + WDL Team
• Where might I download an hapmap for experimenting with GATK

  Answered 239 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2016Ask the GATK team
• MuTect2 Best Practice

  Accepted Answer 843 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2016Ask the GATK team
• Can we implement GATK/Queue on google hadoop?

  Answered 1.4K views 10 comments 0 points Most recent by Geraldine_VdAuwera August 2016Ask the GATK team
• Picard MarkDuplicates vs samtools rmdup for variant calling with GATK

  Accepted Answer 3K views 4 comments 0 points Most recent by shlee July 2016Ask the GATK team
• Nightly build: SelectVariants doesn't appear to work on Haploid VCFs

  Accepted Answer 212 views 2 comments 0 points Most recent by Redmar_van_den_Berg June 2016Ask the GATK team
• What does one do with the raw VCF output of joint genotyping many gVCF files?

  Accepted Answer 1.2K views 5 comments 0 points Most recent by Sheila May 2016Ask the GATK team
• MarkDuplicates on reads with different lengths

  Accepted Answer 408 views 5 comments 0 points Most recent by SvyatoslavSidorov April 2016Ask the GATK team
• PCR indel model for HaplotypeCaller

  Accepted Answer 639 views 6 comments 0 points Most recent by mglclinical April 2016Ask the GATK team
• Second run of BaseRecalibrator in parallel with HaplotypeCaller

  Accepted Answer 437 views 8 comments 0 points Most recent by SvyatoslavSidorov March 2016Ask the GATK team
• AnalyzeCovariates fails in a strange way

  Accepted Answer 207 views 2 comments 0 points Most recent by SvyatoslavSidorov March 2016Ask the GATK team
• CatVariants does not combine header

  Accepted Answer 267 views 3 comments 0 points Most recent by Geraldine_VdAuwera February 2016Ask the GATK team
• RealignerTargetCreator complains about too high quality score

  Accepted Answer 1.1K views 4 comments 0 points Most recent by SvyatoslavSidorov February 2016Ask the GATK team
• Error in force calling variants using HaplotypeCaller

  Answered 421 views 8 comments 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• Custom Walker Distribution and command line

  Answered 221 views 2 comments 0 points Most recent by magicDGS November 2015Ask the GATK team
• GATK SelectVariants RUNTIME ERROR

  Answered 526 views 3 comments 0 points Most recent by trentprall September 2015Ask the GATK team
• Cannot retrieve file pointer positions in SAM file

  Accepted Answer 310 views 4 comments 0 points Most recent by ahulse August 2015Ask the GATK team
• Error: Can't connect to window server - not enough permissions, when running "RealignerTargetCreator

  Answered 1.1K views 5 comments 0 points Most recent by Geraldine_VdAuwera April 2015Ask the GATK team
• incompatible chromosome coordinates in dbsnp and reference file for UnifiedGenotyper

  291 views 2 comments 0 points Most recent by max_shpak March 2015Ask the GATK team
• Using Intervals -L Question

  Accepted Answer 549 views 3 comments 0 points Most recent by thibault February 2015Ask the GATK team
• Question about the roadmap development and optimization of GATK

  451 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 2015Ask the GATK team
• DepthofCoverage: More rows in output that in target file

  Accepted Answer 272 views 2 comments 0 points Most recent by mehar November 2014Ask the GATK team
• Fail to apply --filterExpression of VariantFiltration

  Accepted Answer 1.2K views 2 comments 0 points Most recent by xiayanok October 2014Ask the GATK team
• CombineVariants prioritize option

  Accepted Answer 1.2K views 19 comments 1 point Most recent by Geraldine_VdAuwera October 2014Ask the GATK team
• New doc for newbies: GATK command syntax

  225 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2014Announcements
• What is the structure of a GATK command?

  814 views 0 comments 0 points Started by Geraldine_VdAuwera October 2014 Frequently Asked Questions
• Error when running HaplotypeCaller

  Answered 245 views 1 comment 0 points Most recent by Sheila September 2014Ask the GATK team
• Badly formed genome loc ERROR

  Accepted Answer 970 views 3 comments 0 points Most recent by Sheila August 2014Ask the GATK team
• How to use GATK for RNA-seq analysis?

  Answered 2.6K views 15 comments 0 points Most recent by Geraldine_VdAuwera May 2014Ask the GATK team
• 3.1-1 CatVariants walker not found

  Accepted Answer 488 views 2 comments 0 points Most recent by eroberson April 2014Ask the GATK team
• HaplotypeCaller takes too long

  Answered 750 views 9 comments 0 points Most recent by Geraldine_VdAuwera October 2013Ask the GATK team
• if I have a list of input files, how do I set the output file names?

  Answered 211 views 2 comments 0 points Most recent by rcholic July 2013Ask the GATK team
• How to get deletions?

  Answered 476 views 6 comments 0 points Most recent by Geraldine_VdAuwera June 2013Ask the GATK team
• PhasebyTransmission error concerning Genotype Likelihood score

  Accepted Answer 374 views 8 comments 0 points Most recent by Geraldine_VdAuwera June 2013Ask the GATK team
• -L option file formats

  Accepted Answer 1.7K views 3 comments 0 points Most recent by tommycarstensen April 2013Ask the GATK team
• [GATK PrintReads error]Key 1036 is too large for dimension 2 (max is 1001)

  581 views 5 comments 0 points Most recent by Geraldine_VdAuwera March 2013Ask the GATK team
• Running BaseRecalibrator

  Accepted Answer 3.1K views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2012Ask the GATK team
• I'm not able to run this program on my Mac

  Accepted Answer 527 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2012Ask the GATK team
• GATK temporary directory

  Accepted Answer 3.3K views 2 comments 0 points Most recent by trickytank October 2012Ask the GATK team