Ask the GATK team

• Handling Multimappers

  Answered 528 views 4 comments 0 points Most recent by bruce01 July 2014Ask the GATK team
• Supported SNPeff version with GATK

  Answered 477 views 9 comments 0 points Most recent by Gesseca January 2015Ask the GATK team
• New To GATK , WGS Germline/Tumor Data ~ OK for GATK ?

  Answered 99 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• VariantRecalibrator raising the number of variants used to train the negative model question

  Answered 306 views 5 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• pre-processing reads and non-model BQSR

  Answered 681 views 4 comments 0 points Most recent by ritamichelle July 2014Ask the GATK team
• Argument with name 'knownSites' isn't defined

  1.3K views 5 comments 0 points Most recent by palmeira September 2014Ask the GATK team
• bam to fasta

  Answered 1.1K views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• StrandBiasbySample, FisherStrand Annotation

  Answered 1K views 14 comments 1 point Most recent by Sheila September 2016Ask the GATK team
• What's the base of VQSLOD

  Answered 278 views 2 comments 0 points Most recent by tennis_music July 2014Ask the GATK team
• "FilteredInAll" VariantEval category

  Question 498 views 8 comments 0 points Most recent by eflynn90 July 2014Ask the GATK team
• Help need to fix the error while running DepthofCoverage

  Answered 129 views 1 comment 0 points Most recent by pdexheimer July 2014Ask the GATK team
• What factors influence the runtime of filtering vcf files?

  Answered 130 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• confusion about this documents: How should I interpret VCF files produced by the GATK?

  Answered 510 views 11 comments 0 points Most recent by dainguyen December 2014Ask the GATK team
• CPU usage

  Answered 346 views 5 comments 0 points Most recent by TechnicalVault November 2014Ask the GATK team
• ContESt for WGS data

  Answered 420 views 15 comments 0 points Most recent by Sheila September 2016Ask the GATK team
• Parallelization at core level for RealignerTargetCreator and IndelRealigner?

  Answered 340 views 5 comments 0 points Most recent by Sheila July 2014Ask the GATK team
• possible issue with VCF files made by GenotypeGVCFs in 3.2-2??

  Answered 388 views 4 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Maven build error in current git

  Answered 991 views 7 comments 0 points Most recent by Geraldine_VdAuwera August 2014Ask the GATK team
• How Can I Get strand Bias Imformation From Mutect?

  Answered 943 views 5 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Problem running RealignerTargetCreator

  Answered 449 views 2 comments 0 points Most recent by gedoardo83 July 2014Ask the GATK team
• DiagnoseTargets: NO_READS and COVERAGE filters

  Answered 303 views 6 comments 0 points Most recent by Sheila August 2014Ask the GATK team
• HaplotypeCaller call SNP and indel .

  398 views 12 comments 0 points Most recent by xiaoyun July 2014Ask the GATK team
• Variant Calling of a personal genome : USAGE question

  Answered 228 views 4 comments 0 points Most recent by Nilaksha July 2014Ask the GATK team
• Haplotype Caller - incorrect DP with medium coverage data and missed tri-allelic sites

  Answered 564 views 6 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• depth of coverage link

  Answered 579 views 5 comments 0 points Most recent by estif74 July 2014Ask the GATK team
• Expected runtime for GenotypeGVCFs -- taking long time

  Answered 692 views 6 comments 0 points Most recent by pdexheimer July 2014Ask the GATK team
• realignment of bam files

  Answered 161 views 7 comments 0 points Most recent by ratanchopra July 2014Ask the GATK team
• QUAL vs. Ts/Tv correlations , for hgh QUAL values

  Answered 729 views 8 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• BaseRecalibrator : problem in vcf files

  Answered 443 views 1 comment 0 points Most recent by thibault July 2014Ask the GATK team
• Resource bundle location

  Answered 351 views 5 comments 0 points Most recent by deepak_grover July 2014Ask the GATK team
• Resource bundle location

  Answered 103 views 2 comments 0 points Most recent by Geraldine_VdAuwera September 2014Ask the GATK team
• Variant Recalibration failing

  Answered 1.2K views 27 comments 0 points Most recent by shlee May 9Ask the GATK team
• Issues with Base Quality Score Recalibration

  Answered 575 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• dbSNP138 vs dbSNP141 version in GATK Bundle

  Answered 1.1K views 5 comments 0 points Most recent by Sheila August 2014Ask the GATK team
• Can -nct/-nt option in UnifiedGenotyper make different vcfs?

  Answered 538 views 1 comment 0 points Most recent by Sheila July 2014Ask the GATK team
• Unified genotyper

  Answered 124 views 1 comment 0 points Most recent by Sheila July 2014Ask the GATK team
• 0/0 genotypes with no associated AD

  Answered 222 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• select variants documentation

  Answered 298 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• which input files for IndelRealigner and BaseRecalibrator?

  Answered 1.1K views 2 comments 0 points Most recent by KinMok July 2014Ask the GATK team
• GenotypeGVCF -allSites --includeNonVariantSites option

  Answered 475 views 2 comments 0 points Most recent by prepagam July 2014Ask the GATK team
• The reference fasta for hg19 from your resource bundle is not readable by PicardTools reorder

  Answered 1.1K views 4 comments 0 points Most recent by Geraldine_VdAuwera November 2014Ask the GATK team
• HaplotypeCaller active regions

  Answered 1K views 5 comments 0 points Most recent by Geraldine_VdAuwera October 2015Ask the GATK team
• GenotypeGVCFs remaining runtime estimate incorrect

  Question 494 views 4 comments 0 points Most recent by tommycarstensen July 2014Ask the GATK team
• GT:AD:DP:GQ:PL instead of GT:DP:GQ when merging two vcf files with more than two alleles

  Answered 939 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• I have a error message that Index 25, size 8.

  Answered 298 views 6 comments 0 points Most recent by weiqiang July 2014Ask the GATK team
• CatVariants not working?

  Answered 1.3K views 7 comments 0 points Most recent by gipelttil July 2014Ask the GATK team
• combineGVCF bug?

  Answered 636 views 19 comments 0 points Most recent by jhomsy August 2014Ask the GATK team
• IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2)

  Answered 776 views 7 comments 0 points Most recent by Geraldine_VdAuwera November 2014Ask the GATK team
• low quality variants

  Answered 179 views 2 comments 0 points Most recent by Jayce July 2014Ask the GATK team
• problem with queue job reports in 3.2-0

  Answered 469 views 3 comments 0 points Most recent by jam July 2014Ask the GATK team
• NHLBI Exome Sequencing Project ESP indel

  Answered 469 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Loss of Reads in HCMappingQualityFilter

  Answered 896 views 21 comments 0 points Most recent by Geraldine_VdAuwera December 2016Ask the GATK team
• Problem building gatk-protected from github

  Answered 1.2K views 7 comments 0 points Most recent by Johan_Dahlberg July 2014Ask the GATK team
• Recall variants with haplotypeCaller

  Answered 174 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• AD field doesn't update after merging GVCF files with GenotypeGVCFs

  Answered 281 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Oncotator Splice Isoform Annotations

  Answered 254 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Splice Isoform Annotations in Oncotator

  Question 88 views 0 comments 0 points Started by emcmillan July 2014 Ask the GATK team
• Realigner Target Creator does not realign correctly with known indel

  Answered 654 views 7 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Indelrealignment

  Answered 438 views 7 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• GVCF error - Argument emitRefConfidence has a bad value

  Answered 515 views 4 comments 0 points Most recent by vifehe April 2015Ask the GATK team
• HAPLOTYPER ROI PARALELITATION

  72 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• How do you calculate MQ?

  Answered 752 views 7 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Known sites for Base Recalibration and Variant Quality Score Recalibration

  Answered 817 views 21 comments 0 points Most recent by Geraldine_VdAuwera January 2015Ask the GATK team
• Cannot downsample using printReads an -dcov parameter. No effect over original bam observed.

  Answered 776 views 10 comments 0 points Most recent by TechnicalVault December 2014Ask the GATK team
• Varinat calling from Multisample RNAseq data???

  Answered 337 views 2 comments 0 points Most recent by tejas July 2014Ask the GATK team
• ClippingRankSumTest - Hard clipped bases only

  Answered 106 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• RegenotypeVariants

  Answered 206 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Understanding the Output from GenotypeGVCFs

  Answered 194 views 2 comments 0 points Most recent by JonathonBlake July 2014Ask the GATK team
• VariantEval and FunctionalClass: missing SNP class data from tables - any help for newbie.

  Answered 187 views 2 comments 0 points Most recent by drmtbishop July 2014Ask the GATK team
• Zero INDELs from UnifiedGenotyper from 74 samples

  Answered 161 views 2 comments 0 points Most recent by tinu July 2014Ask the GATK team
• Anyone attending the ISMB 2014 conference July 13 - 15 here?

  Answered 159 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• How to get the number of forward/reverse reads in the final VCF output?

  Answered 356 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Variant discovery in aneuploid organisms

  Answered 358 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Sensible ways to split CombineGVCFs

  Answered 737 views 13 comments 1 point Most recent by Geraldine_VdAuwera July 23Ask the GATK team
• How to make RealignerTargetCreator more sensitive

  Answered 240 views 7 comments 0 points Most recent by fborja July 2014Ask the GATK team
• VQSR filter

  Answered 181 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• HaplotypeCaller and GPU

  Answered 392 views 2 comments 0 points Most recent by kwyattm July 2014Ask the GATK team
• long indel by GATK unified genotyper

  Answered 175 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• GATK-BaseRecalibrator run error

  102 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• Unified Genotyper: Maximum sensitivity

  Answered 297 views 5 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• IndelRealigner -nWayOut: Possible to specify output directory?

  Answered 862 views 7 comments 0 points Most recent by Sheila October 2014Ask the GATK team
• GATK Variant caller- unifiedGenotyper input BAM file

  186 views 4 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• SplitNCigarReads complains about N in CIGAR

  Answered 1.7K views 16 comments 0 points Most recent by Geraldine_VdAuwera September 2016Ask the GATK team
• ERROR MESSAGE: For input string: "." when validating variants

  7.6K views 2 comments 0 points Most recent by baesc July 2014Ask the GATK team
• VQSR VariantRecalibrator Rplot

  Answered 477 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team
• BQSR: empirical vs. recorded base quality

  Answered 391 views 4 comments 0 points Most recent by mayaab July 2014Ask the GATK team
• VariantFiltration and VariantRecalibrator

  Answered 349 views 5 comments 0 points Most recent by Sheila July 2014Ask the GATK team
• How to estimate heap size (-Xmx) necessary to call variants using Unified Genotyper?

  Answered 993 views 11 comments 0 points Most recent by Geraldine_VdAuwera May 2015Ask the GATK team
• How do I get Indelocator?

  Answered 346 views 7 comments 0 points Most recent by egeulgen August 2015Ask the GATK team
• BAM malformed verification tool?

  Answered 182 views 1 comment 0 points Most recent by Sheila July 2014Ask the GATK team
• run CombineGVCFs per chromosome and merge with CatVariants?

  Answered 952 views 8 comments 0 points Most recent by Lavanya May 2015Ask the GATK team
• GENOTYPE_GIVEN_ALLELES mode in HaplotypeCaller

  Answered 671 views 3 comments 0 points Most recent by Sheila October 2014Ask the GATK team
• Input files reads and reference have incompatible contigs

  Answered 679 views 10 comments 0 points Most recent by wukhan September 2015Ask the GATK team
• About the binned quality scores of Illumina Hiseq X 10

  Answered 636 views 2 comments 0 points Most recent by luciaUY July 2014Ask the GATK team
• Combine gVFC and GenotypeGVCFs

  Answered 428 views 6 comments 0 points Most recent by tberner July 2014Ask the GATK team
• merging bam files for an individual

  Answered 1K views 3 comments 0 points Most recent by eflynn90 July 2014Ask the GATK team
• Oncotator run error: Could not find config file (maflite_input.config)

  Answered 375 views 2 comments 0 points Most recent by pratikchandrani July 2014Ask the GATK team
• can I strip out BD/BI stings after creating gvcf in the new 3.1 workflow?

  Answered 259 views 6 comments 0 points Most recent by Geraldine_VdAuwera July 2014Ask the GATK team