gatk

Discussion List

• Should SplitNCigarReads still be run even though BWA was the aligner used?

  Question 3 views 0 comments 0 points Started by claudiadast 8:21PM Ask the GATK team
• VCF from RNA-seq data

  Accepted Answer 37 views 6 comments 0 points Most recent by bhanuGandham March 25Ask the GATK team
• Java FileNotFoundError while executing gatk4

  Accepted Answer 21 views 2 comments 0 points Most recent by lakhujanivijay March 18Ask the GATK team
• GATK 4.1.0.0 Release

  480 views 7 comments 0 points Most recent by SkyWarrior February 22Announcements
• SelectVariants Starts Traversal but Does not Progress, High CPU Usage

  Answered 41 views 9 comments 0 points Most recent by AdelaideR February 13Ask the GATK team
• How to output AD ref and alt in separate columns with VariantsToTable

  Accepted Answer 32 views 5 comments 0 points Most recent by steve1 February 1Ask the GATK team
• IntervalListTools UNION corner case: doesn't keep all name fields if merged coordinates are same

  Answered 19 views 5 comments 0 points Most recent by bhanuGandham January 23Ask the GATK team
• guidelines for BAM realignment in GATK 4

  Accepted Answer 56 views 1 comment 0 points Most recent by bhanuGandham January 7Ask the GATK team
• spark-master is not a recognized option

  Answered 63 views 1 comment 0 points Most recent by bhanuGandham December 2018Ask the GATK team
• Example from video (AWS Batch + GATK WDL/Cromwell) does not work for me

  Answered 131 views 4 comments 0 points Most recent by Ruchi December 2018Ask the Cromwell + WDL Team
• about argument presentation

  Answered 39 views 5 comments 0 points Most recent by AdelaideR November 2018Ask the GATK team
• Errors for MuTect2_pon: CalculateContamination

  Answered 65 views 5 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• About java threads in GATK

  Accepted Answer 322 views 10 comments 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• Using GATK pipelines?

  Accepted Answer 19 views 0 comments 0 points Started by tonny91 October 2018 Ask the GATK team
• Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

  Answered 453 views 3 comments 0 points Most recent by shlee October 2018Ask the GATK team
• generate figure from BQSR gatk version 4

  Accepted Answer 127 views 3 comments 0 points Most recent by dbecker October 2018Ask the GATK team
• Should I provide the exome target list (-L argu) even while calling gVCF file using Haplotypecaller?

  Accepted Answer 786 views 37 comments 0 points Most recent by shlee October 2018Ask the GATK team
• ALT * no deletion

  Accepted Answer 48 views 1 comment 0 points Most recent by shlee October 2018Ask the GATK team
• select intersection, merged VCF files

  Answered 88 views 1 comment 0 points Most recent by shlee October 2018Ask the GATK team
• BQSR -knownSites

  Accepted Answer 100 views 1 comment 0 points Most recent by bhanuGandham September 2018Ask the GATK team
• From one sample to multiple samples

  Accepted Answer 276 views 4 comments 0 points Most recent by shuangBroad September 2018Ask the Cromwell + WDL Team
• MuTect2: Reference name for '3223094' not found in sequence dictionary

  Answered 65 views 6 comments 0 points Most recent by michaelmc September 2018Ask the GATK team
• GATK analysis using Bam files after BWA alignment

  Accepted Answer 73 views 5 comments 0 points Most recent by KateN September 2018Ask the FireCloud Team
• AlleleBalance changes

  Accepted Answer 40 views 5 comments 0 points Most recent by bgrenier August 2018Ask the GATK team
• FilterMutectCalls did not give any records with 'PASS' in the filter field

  Answered 61 views 7 comments 0 points Most recent by Sheila August 2018Ask the GATK team
• How to get a variant's abundance from calling file?

  Accepted Answer 27 views 1 comment 0 points Most recent by Sheila August 2018Ask the GATK team
• Running HaplotypeCaller in GATK

  Answered 229 views 1 comment 0 points Most recent by Sheila August 2018Ask the GATK team
• Invalid SAM?

  Answered 83 views 1 comment 0 points Most recent by Sheila August 2018Ask the GATK team
• Variant Calling

  Accepted Answer 23 views 1 comment 0 points Most recent by dbecker August 2018Ask the GATK team
• the number of reads of diploidy, triploidy and tetraploidy

  Answered 37 views 1 comment 0 points Most recent by dbecker August 2018Ask the GATK team
• it's a bug for the calculation of Mutect2 allele frequency ?

  Answered 978 views 16 comments 0 points Most recent by Sheila July 2018Ask the GATK team
• A USER ERROR has occurred: 'CalculateTargetCoverage' is not a valid command.

  Accepted Answer 132 views 1 comment 0 points Most recent by shlee July 2018Ask the GATK team
• Fire-dollar-genome workflow - "does not have storage.objects.get access to" error

  Accepted Answer 121 views 11 comments 0 points Most recent by Bingley June 2018Ask the FireCloud Team
• "UKNOWN" zygosity in CSV file

  Answered 110 views 1 comment 0 points Most recent by Sheila June 2018Ask the GATK team
• UnifiedGenotyper error: Somehow the requested coordinate is not covered by the read.

  Answered 4.6K views 77 comments 0 points Most recent by macko.tipor June 2018Ask the GATK team
• Five-dollar-genome workflow failed: HaplotypeCaller4:39:1 exited with return code 1 which has not be

  Answered 86 views 7 comments 0 points Most recent by Bingley June 2018Ask the FireCloud Team
• How to keep unique sample ID when combining gvcf files?

  Answered 66 views 1 comment 0 points Most recent by Sheila June 2018Ask the GATK team
• VCF contigs don't match reference genome

  Accepted Answer 64 views 4 comments 0 points Most recent by Sheila June 2018Ask the GATK team
• How to relax parameters in GenotypeGVCFs to get more variants?

  Answered 139 views 16 comments 0 points Most recent by Sheila June 2018Ask the GATK team
• Increase marker or point size for PlotDenoisedCopyRatios?

  Accepted Answer 47 views 1 comment 0 points Most recent by shlee May 2018Ask the GATK team
• How does the BQSR step not create bias in SNP detection?

  Accepted Answer 86 views 2 comments 0 points Most recent by lfall May 2018Ask the GATK team
• BQSR for RNA-seq data

  Accepted Answer 112 views 2 comments 0 points Most recent by lfall May 2018Ask the GATK team
• Let the 2018 GATK workshop season begin!

  256 views 2 comments 0 points Most recent by Geraldine_VdAuwera May 2018Announcements
• GenotypeGVCFs Estimated Runtime 5.9 YEARS!!!

  Answered 151 views 2 comments 0 points Most recent by maierpa April 2018Ask the GATK team
• GATK gradlew bundle Error

  Answered 72 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2018Ask the GATK team
• How to narrow down the variants after VQSR in germline variant discovery and filtering?

  Answered 35 views 3 comments 0 points Most recent by Sheila April 2018Ask the GATK team
• GATK3.8 vs GATK4 HaplotypeCaller

  Answered 230 views 1 comment 0 points Most recent by Sheila April 2018Ask the GATK team
• VariantFiltration: how to filter samples where less then 95% of reads agree with the called genotype

  Accepted Answer 405 views 3 comments 0 points Most recent by Sheila April 2018Ask the GATK team
• no. of cores utilization in haplotypcaller in GVCF mode

  Accepted Answer 385 views 10 comments 1 point Most recent by prasundutta87 March 2018Ask the GATK team
• Truncated Bam error in recalibrated bam file

  Accepted Answer 74 views 7 comments 0 points Most recent by SkyWarrior March 2018Ask the GATK team
• Build Error in Mutect: GATK-Framework

  Answered 57 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• Standard practice for VCF filtering for the purpose of fingerprinting via proportion IBS?

  Answered 155 views 10 comments 0 points Most recent by shlee March 2018Ask the GATK team
• WDL script is not copying the index files for the reference genome from its directory

  Accepted Answer 37 views 2 comments 0 points Most recent by ChrisL March 2018Ask the Cromwell + WDL Team
• Can GATK accepts more than one bed file while computing depth of coverage?

  Answered 56 views 3 comments 0 points Most recent by shlee March 2018Ask the GATK team
• Picard AddOrReplaceReadGroups Error: Read CIGAR M operator maps off end of reference

  Accepted Answer 95 views 3 comments 0 points Most recent by shlee March 2018Ask the GATK team
• Not calling all sites in gvcf option (bp_resolution)

  Answered 51 views 1 comment 0 points Most recent by shlee March 2018Ask the GATK team
• DepthOfCoverage fails with java.lang.ArithmeticException: / by zero

  Answered 58 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• Deleting intermediate files

  Answered 486 views 12 comments 0 points Most recent by dinvlad March 2018Ask the Cromwell + WDL Team
• Combine Variants throwing a bug error

  Answered 104 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2018Ask the Cromwell + WDL Team
• CombineGVCFs - All alleles are missing

  Accepted Answer 677 views 9 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• VariantAnnotator is not annotating variants with InbreedingCoeff

  Answered 105 views 1 comment 0 points Most recent by Sheila February 2018Ask the GATK team
• Can I use GATK workflow for plant (Cannabis) to detect variants?

  Accepted Answer 83 views 5 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• [Publish] Publish my own WDL including GATK

  Accepted Answer 129 views 3 comments 0 points Most recent by KateN February 2018Ask the FireCloud Team
• A GATK RUNTIME ERROR, Invalid alignment found, alignmentStart > alignemntEnd

  Accepted Answer 42 views 4 comments 0 points Most recent by hjzhou February 2018GenomeSTRiP
• Where to find CreateSequenceDictionary.jar?

  Accepted Answer 1.6K views 4 comments 0 points Most recent by Prisca_Thami February 2018Ask the GATK team
• Cancer variant calling workflow with mutect and changes/additions to the GATK best practices

  Answered 2.4K views 8 comments 0 points Most recent by Geraldine_VdAuwera February 2018MuTect v1
• Is there a consensus minimum number of probes to use as cutoff for GATK CNV pipeline (exome)

  Accepted Answer 94 views 1 comment 0 points Most recent by slee January 2018Ask the GATK team
• help with picard CollectHsMetrics

  Answered 113 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 139 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 164 views 3 comments 0 points Most recent by shlee November 2017Ask the GATK team
• Empty file with VariantsToVCF

  Answered 915 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 115 views 1 comment 0 points Most recent by Redmar_van_den_Berg November 2017Ask the GATK team
• bcbio configuration file (bcbio_system.yaml)

  Answered 125 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 94 views 1 comment 0 points Most recent by Sheila October 2017Ask the GATK team
• Mutect 2 java memory shortage: a case study.

  Answered 152 views 1 comment 0 points Most recent by SkyWarrior October 2017Ask the GATK team
• Do you use GATK? Take this survey, win a prize!

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

  Answered 260 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 74 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 81 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 134 views 2 comments 0 points Most recent by Sheila September 2017Ask the GATK team
• Testing different capture reaction template

  Accepted Answer 224 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 93 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 102 views 3 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• Clean version of dbSNP in the GATK resource bundle

  Answered 317 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 354 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 125 views 3 comments 0 points Most recent by cbao August 2017Ask the FireCloud Team
• SnpEff html and .vcf file result are not matching

  Answered 91 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 95 views 1 comment 0 points Most recent by Sheila August 2017Ask the GATK team
• Regarding Gatk output

  Answered 36 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 168 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 435 views 11 comments 0 points Most recent by shlee August 2017Ask the GATK team
• Does GATK version 4 support hg19?

  Answered 68 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2017Ask the GATK team
• CalculateGenotypePosteriors (hg19) error

  Accepted Answer 159 views 10 comments 0 points Most recent by sbourgeois July 2017Ask the GATK team
• How to return an Array given as input

  Accepted Answer 207 views 2 comments 0 points Most recent by dbecker July 2017Ask the Cromwell + WDL Team
• Trimming of Adaptor sequence?

  Accepted Answer 795 views 1 comment 0 points Most recent by shlee July 2017Ask the GATK team
• Problemm with hard filtering

  Answered 453 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 87 views 4 comments 0 points Most recent by Sheila June 2017Ask the GATK team
• Error in ValidateSamFile when multiplexing MarkDuplicates

  Accepted Answer 171 views 2 comments 0 points Most recent by Sheila May 2017Ask the GATK team
• GATK best pratices for RNA-seq somatic mutation finding

  Answered 1.1K views 11 comments 0 points Most recent by shlee May 2017Ask the GATK team
• Missing gentoypes despite high number of reads

  Answered 60 views 1 comment 0 points Most recent by Sheila May 2017Ask the GATK team