gatk

Discussion List

• generate figure from BQSR gatk version 4

  Accepted Answer 32 views 3 comments 0 points Most recent by dbecker October 12Ask the GATK team
• Should I provide the exome target list (-L argu) even while calling gVCF file using Haplotypecaller?

  Accepted Answer 532 views 37 comments 0 points Most recent by shlee October 11Ask the GATK team
• Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

  Answered 177 views 2 comments 0 points Most recent by psb21 October 7Ask the GATK team
• ALT * no deletion

  Answered 22 views 1 comment 0 points Most recent by shlee October 1Ask the GATK team
• select intersection, merged VCF files

  Answered 36 views 1 comment 0 points Most recent by shlee October 1Ask the GATK team
• BQSR -knownSites

  Accepted Answer 44 views 1 comment 0 points Most recent by bhanuGandham September 21Ask the GATK team
• From one sample to multiple samples

  Accepted Answer 124 views 4 comments 0 points Most recent by shuangBroad September 10Ask the Cromwell + WDL Team
• MuTect2: Reference name for '3223094' not found in sequence dictionary

  Answered 28 views 6 comments 0 points Most recent by michaelmc September 10Ask the GATK team
• GATK analysis using Bam files after BWA alignment

  Accepted Answer 50 views 5 comments 0 points Most recent by KateN September 6Ask the FireCloud Team
• AlleleBalance changes

  Accepted Answer 20 views 5 comments 0 points Most recent by bgrenier August 29Ask the GATK team
• FilterMutectCalls did not give any records with 'PASS' in the filter field

  Answered 24 views 7 comments 0 points Most recent by Sheila August 27Ask the GATK team
• How to get a variant's abundance from calling file?

  Accepted Answer 16 views 1 comment 0 points Most recent by Sheila August 13Ask the GATK team
• Running HaplotypeCaller in GATK

  Answered 78 views 1 comment 0 points Most recent by Sheila August 12Ask the GATK team
• Invalid SAM?

  Answered 29 views 1 comment 0 points Most recent by Sheila August 4Ask the GATK team
• Variant Calling

  Accepted Answer 16 views 1 comment 0 points Most recent by dbecker August 3Ask the GATK team
• the number of reads of diploidy, triploidy and tetraploidy

  Answered 18 views 1 comment 0 points Most recent by dbecker August 1Ask the GATK team
• it's a bug for the calculation of Mutect2 allele frequency ?

  Answered 693 views 16 comments 0 points Most recent by Sheila July 27Ask the GATK team
• A USER ERROR has occurred: 'CalculateTargetCoverage' is not a valid command.

  Accepted Answer 56 views 1 comment 0 points Most recent by shlee July 5Ask the GATK team
• Fire-dollar-genome workflow - "does not have storage.objects.get access to" error

  Accepted Answer 86 views 11 comments 0 points Most recent by Bingley June 30Ask the FireCloud Team
• "UKNOWN" zygosity in CSV file

  Answered 77 views 1 comment 0 points Most recent by Sheila June 27Ask the GATK team
• UnifiedGenotyper error: Somehow the requested coordinate is not covered by the read.

  Answered 4.4K views 77 comments 0 points Most recent by macko.tipor June 26Ask the GATK team
• Five-dollar-genome workflow failed: HaplotypeCaller4:39:1 exited with return code 1 which has not be

  Answered 62 views 7 comments 0 points Most recent by Bingley June 25Ask the FireCloud Team
• About java threads in GATK

  Accepted Answer 68 views 8 comments 0 points Most recent by prasundutta87 June 25Ask the GATK team
• How to keep unique sample ID when combining gvcf files?

  Answered 27 views 1 comment 0 points Most recent by Sheila June 13Ask the GATK team
• VCF contigs don't match reference genome

  Accepted Answer 30 views 4 comments 0 points Most recent by Sheila June 8Ask the GATK team
• How to relax parameters in GenotypeGVCFs to get more variants?

  Question 62 views 16 comments 0 points Most recent by Sheila June 8Ask the GATK team
• Increase marker or point size for PlotDenoisedCopyRatios?

  Accepted Answer 29 views 1 comment 0 points Most recent by shlee May 24Ask the GATK team
• How does the BQSR step not create bias in SNP detection?

  Accepted Answer 55 views 2 comments 0 points Most recent by lfall May 21Ask the GATK team
• BQSR for RNA-seq data

  Accepted Answer 56 views 2 comments 0 points Most recent by lfall May 17Ask the GATK team
• Let the 2018 GATK workshop season begin!

  207 views 2 comments 0 points Most recent by Geraldine_VdAuwera May 15Announcements
• GenotypeGVCFs Estimated Runtime 5.9 YEARS!!!

  Answered 87 views 2 comments 0 points Most recent by maierpa April 27Ask the GATK team
• GATK gradlew bundle Error

  Answered 53 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 22Ask the GATK team
• How to narrow down the variants after VQSR in germline variant discovery and filtering?

  Answered 27 views 3 comments 0 points Most recent by Sheila April 18Ask the GATK team
• GATK3.8 vs GATK4 HaplotypeCaller

  Answered 156 views 1 comment 0 points Most recent by Sheila April 3Ask the GATK team
• VariantFiltration: how to filter samples where less then 95% of reads agree with the called genotype

  Accepted Answer 343 views 3 comments 0 points Most recent by Sheila April 2Ask the GATK team
• no. of cores utilization in haplotypcaller in GVCF mode

  Accepted Answer 204 views 10 comments 1 point Most recent by prasundutta87 March 31Ask the GATK team
• Truncated Bam error in recalibrated bam file

  Accepted Answer 46 views 7 comments 0 points Most recent by SkyWarrior March 28Ask the GATK team
• Build Error in Mutect: GATK-Framework

  Answered 38 views 1 comment 0 points Most recent by Sheila March 27Ask the GATK team
• Standard practice for VCF filtering for the purpose of fingerprinting via proportion IBS?

  Answered 87 views 10 comments 0 points Most recent by shlee March 26Ask the GATK team
• WDL script is not copying the index files for the reference genome from its directory

  Accepted Answer 30 views 2 comments 0 points Most recent by ChrisL March 23Ask the Cromwell + WDL Team
• Can GATK accepts more than one bed file while computing depth of coverage?

  Answered 41 views 3 comments 0 points Most recent by shlee March 22Ask the GATK team
• Picard AddOrReplaceReadGroups Error: Read CIGAR M operator maps off end of reference

  Accepted Answer 58 views 3 comments 0 points Most recent by shlee March 20Ask the GATK team
• Not calling all sites in gvcf option (bp_resolution)

  Answered 38 views 1 comment 0 points Most recent by shlee March 20Ask the GATK team
• DepthOfCoverage fails with java.lang.ArithmeticException: / by zero

  Answered 36 views 1 comment 0 points Most recent by Sheila March 14Ask the GATK team
• Deleting intermediate files

  Answered 352 views 12 comments 0 points Most recent by dinvlad March 9Ask the Cromwell + WDL Team
• Combine Variants throwing a bug error

  Answered 74 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 7Ask the Cromwell + WDL Team
• CombineGVCFs - All alleles are missing

  Accepted Answer 614 views 9 comments 0 points Most recent by Sheila February 28Ask the GATK team
• VariantAnnotator is not annotating variants with InbreedingCoeff

  Answered 78 views 1 comment 0 points Most recent by Sheila February 27Ask the GATK team
• Can I use GATK workflow for plant (Cannabis) to detect variants?

  Accepted Answer 54 views 5 comments 0 points Most recent by Sheila February 21Ask the GATK team
• [Publish] Publish my own WDL including GATK

  Accepted Answer 121 views 3 comments 0 points Most recent by KateN February 21Ask the FireCloud Team
• A GATK RUNTIME ERROR, Invalid alignment found, alignmentStart > alignemntEnd

  Accepted Answer 30 views 4 comments 0 points Most recent by hjzhou February 20GenomeSTRiP
• Where to find CreateSequenceDictionary.jar?

  Accepted Answer 1.1K views 4 comments 0 points Most recent by Prisca_Thami February 14Ask 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
• Is there a consensus minimum number of probes to use as cutoff for GATK CNV pipeline (exome)

  Accepted Answer 66 views 1 comment 0 points Most recent by slee January 22Ask the GATK team
• help with picard CollectHsMetrics

  Answered 61 views 1 comment 0 points Most recent by Sheila December 2017Ask the GATK team
• [ERROR] the local copy message must have path set.

  Accepted Answer 112 views 7 comments 0 points Most recent by cbao November 2017Ask the FireCloud Team
• In haplotype variant caller for the Influenza virus, do I need to mention or remove any parameters?

  Answered 109 views 3 comments 0 points Most recent by shlee November 2017Ask the GATK team
• Empty file with VariantsToVCF

  Answered 876 views 14 comments 0 points Most recent by sadaf November 2017Ask the GATK team
• Variant reported by GATK is not seen in IGV

  Accepted Answer 77 views 1 comment 0 points Most recent by Redmar_van_den_Berg November 2017Ask the GATK team
• bcbio configuration file (bcbio_system.yaml)

  Answered 93 views 2 comments 0 points Most recent by Geraldine_VdAuwera November 2017Ask the GATK team
• The result of Mutect BAM and vcf is different.

  Answered 71 views 1 comment 0 points Most recent by Sheila October 2017Ask the GATK team
• Mutect 2 java memory shortage: a case study.

  Answered 112 views 1 comment 0 points Most recent by SkyWarrior October 2017Ask the GATK team
• Do you use GATK? Take this survey, win a prize!

  241 views 1 comment 0 points Most recent by Tiffany_at_Broad October 2017Announcements
• SplitNCigarReads results in all reads failing MalformedReadFilter?

  Answered 195 views 8 comments 0 points Most recent by Sheila October 2017Ask the GATK team
• What are the parameters used by GATK to define a SNP?

  Answered 61 views 1 comment 1 point Most recent by Sheila September 2017Ask the GATK team
• Should I remove unmapped bam files from the data for variant calling analysis?

  Accepted Answer 63 views 2 comments 0 points Most recent by snijesh September 2017Ask the GATK team
• When I call Indels from my vcf file using GATK analysis tools I ger an Error!

  Answered 95 views 2 comments 0 points Most recent by Sheila September 2017Ask the GATK team
• Testing different capture reaction template

  Accepted Answer 208 views 13 comments 0 points Most recent by Sheila September 2017Ask the GATK team
• How to make results from GAT4.beta.3 "HaplotypeCaller" comparable to GATK2.7's "UnifiedGenotyper"?

  Answered 83 views 2 comments 0 points Most recent by Geraldine_VdAuwera August 2017Ask the GATK team
• how to choose sequencing depth for FFPE and cfDNA tumor sample for MuTect2 ?

  Answered 83 views 3 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• Clean version of dbSNP in the GATK resource bundle

  Answered 269 views 4 comments 0 points Most recent by Geraldine_VdAuwera August 2017Ask the GATK team
• what's difference between a read marked by "sam FLAG 1024" and marked by " PG:markduplicates" ?

  Accepted Answer 230 views 5 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• [PoN] What kind of data is in the PoN named "final_summed_tokens.hist.bin"

  Accepted Answer 82 views 3 comments 0 points Most recent by cbao August 2017Ask the FireCloud Team
• SnpEff html and .vcf file result are not matching

  Answered 74 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 2017Ask the GATK team
• what's the difference if do IndelRealigner first,then to bqsr ?

  Answered 72 views 1 comment 0 points Most recent by Sheila August 2017Ask the GATK team
• Regarding Gatk output

  Answered 31 views 1 comment 0 points Most recent by Sheila August 2017Ask the GATK team
• how to set the value "--contamination_fraction_to_filter" of Mutect2 ?

  Answered 129 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 2017Ask the GATK team
• what's the difference between mutect and GATK-Mutect ?

  Answered 341 views 11 comments 0 points Most recent by shlee August 2017Ask the GATK team
• Does GATK version 4 support hg19?

  Answered 51 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2017Ask the GATK team
• CalculateGenotypePosteriors (hg19) error

  Accepted Answer 140 views 10 comments 0 points Most recent by sbourgeois July 2017Ask the GATK team
• How to return an Array given as input

  Accepted Answer 154 views 2 comments 0 points Most recent by dbecker July 2017Ask the Cromwell + WDL Team
• Trimming of Adaptor sequence?

  Accepted Answer 557 views 1 comment 0 points Most recent by shlee July 2017Ask the GATK team
• Problemm with hard filtering

  Answered 360 views 22 comments 0 points Most recent by Sheila June 2017Ask the GATK team
• I have been trying to run the following command for Queue.jar. But its not compiling properly.

  Answered 69 views 4 comments 0 points Most recent by Sheila June 2017Ask the GATK team
• Error in ValidateSamFile when multiplexing MarkDuplicates

  Accepted Answer 119 views 2 comments 0 points Most recent by Sheila May 2017Ask the GATK team
• GATK best pratices for RNA-seq somatic mutation finding

  Answered 888 views 11 comments 0 points Most recent by shlee May 2017Ask the GATK team
• Missing gentoypes despite high number of reads

  Answered 52 views 1 comment 0 points Most recent by Sheila May 2017Ask the GATK team
• Running MuTect error Malformed walker argument: Could not find walker with name

  Accepted Answer 911 views 7 comments 0 points Most recent by Sheila May 2017MuTect v1
• MNP detection using ReadBackedPhasing

  Answered 193 views 3 comments 0 points Most recent by Sheila May 2017Ask the GATK team
• GATK supporting reads versus IGV display

  Accepted Answer 149 views 3 comments 0 points Most recent by cpsosa0006 April 2017Ask the GATK team
• how to build GATK 3.7 ?

  212 views 3 comments 0 points Most recent by Geraldine_VdAuwera April 2017Ask the GATK team
• REGARDING COMBINING VARIANTS IN CLOUDMAP IN GALAXY

  54 views 1 comment 0 points Most recent by Sheila April 2017Ask the GATK team
• GATK DepthOfCoverage

  Accepted Answer 420 views 2 comments 0 points Most recent by vesna_pajic April 2017Ask the GATK team
• Default value of HaplotypeCaller

  Answered 101 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2017Ask the GATK team
• Out of space when running SplitNCigarReads

  Answered 668 views 9 comments 0 points Most recent by Sheila March 2017Ask the GATK team
• Best Practices for Batch Calling Malaria

  Accepted Answer 153 views 3 comments 0 points Most recent by virpatel524 March 2017Ask the GATK team
• Can i use Apache spark to submit job to GATK?

  Answered 320 views 6 comments 0 points Most recent by Geraldine_VdAuwera March 2017Ask the GATK team
• Trio analysis using the GATK toolbox

  Accepted Answer 269 views 2 comments 0 points Most recent by alphahmed March 2017Ask the GATK team
• AD different with DP

  Accepted Answer 210 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2017MuTect v1
• Error in AnalyzeCovariates

  Answered 112 views 1 comment 0 points Most recent by Sheila March 2017Ask the GATK team