gatk

Discussion List

• GATK_docker image to run Mutect2

  Answered 16 views 4 comments 0 points Most recent by Tiffany_at_Broad October 22Ask the GATK team
• BAM file generated by GATK HaplotypeCaller shows duplicates, not fixed by Picard FixMateInformation

  Question 12 views 0 comments 0 points Started by elcortegano October 17 Ask the GATK team
• Funcotator timing expectations

  Accepted Answer 31 views 4 comments 0 points Most recent by bhanuGandham September 26Ask the GATK team
• AddOrReplaceReadGroups error even when all details are provided

  Answered 25 views 2 comments 0 points Most recent by bhanuGandham September 16Ask the GATK team
• Alternative resources for Mutect2/GetPileupSummaries when dealing with genome data

  Answered 45 views 3 comments 0 points Most recent by akovalsk September 13Ask the GATK team
• Setting a specific seed when using GATK

  Accepted Answer 40 views 3 comments 0 points Most recent by bhanuGandham August 19Ask the GATK team
• Different resource for Mutect2/GetPileupSummaries when dealing with genome data

  14 views 0 comments 0 points Started by michaelmc August 14 Zoo & Garden
• Using GATK SelectVariants to filter based on calculated allele frequency

  Answered 95 views 4 comments 0 points Most recent by bhanuGandham August 12Ask the GATK team
• How do MuTect1.1.4 and MuTect2 differ in Tumor only mode (no matched control) variant calling

  Answered 47 views 1 comment 0 points Most recent by davidben August 9Ask the GATK team
• GATK - HaplotypeCaller is so slow, is this normal??

  Accepted Answer 1.8K views 11 comments 0 points Most recent by lakhujanivijay July 31Ask the GATK team
• GATK 4.1.0.0 Release

  1.1K views 9 comments 0 points Most recent by bhanuGandham July 29Announcements
• VQSR filtering and dbSNP

  Answered 46 views 2 comments 0 points Most recent by jush July 24Ask the GATK team
• Piped command for realignment of BAM files

  Question 26 views 1 comment 0 points Most recent by bshifaw July 23Ask the GATK team
• why variant callers's (GATK3.8 and GATK 4.0) results are different ?

  Question 20 views 0 comments 0 points Started by Shariq June 21 Ask the GATK team
• GATK variant calling

  Answered 146 views 11 comments 0 points Most recent by bshifaw June 19Ask the GATK team
• Variant filtration by allelic balance bias

  Answered 43 views 1 comment 0 points Most recent by bhanuGandham June 10Ask the GATK team
• VariantFiltration: how to filter samples where less then 95% of reads agree with the called genotype

  Accepted Answer 485 views 4 comments 0 points Most recent by Nolan_Shelley June 10Ask the GATK team
• Error with GenomicsDBImport input file

  Accepted Answer 32 views 1 comment 0 points Most recent by nparmalee June 6Ask the GATK team
• SelectVariants - java.lang.IllegalStateException: Allele in genotype not in the variant context

  Answered 57 views 2 comments 0 points Most recent by mpmachado June 5Ask the GATK team
• AD allele depth interpretation

  Answered 58 views 1 comment 0 points Most recent by Amir_Ariff June 3Ask the GATK team
• Invalid SAM?

  Answered 151 views 3 comments 0 points Most recent by AdelaideR May 20Ask the GATK team
• MergeBamAlignment warning in the best practice pipeline

  Accepted Answer 93 views 5 comments 0 points Most recent by AdelaideR May 16Ask the GATK team
• Picard AddOrReplaceGroups for singly biological sample

  Accepted Answer 42 views 5 comments 0 points Most recent by bshifaw May 7Ask the GATK team
• Mapping a locus to a chromosome in a genome

  Answered 16 views 1 comment 0 points Most recent by bhanuGandham May 3Ask the GATK team
• GATK IndelRealigner error: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated

  Answered 56 views 1 comment 0 points Most recent by bshifaw May 3Ask the GATK team
• Standard practice for VCF filtering for the purpose of fingerprinting via proportion IBS?

  Answered 257 views 11 comments 0 points Most recent by golharam April 26Ask the GATK team
• Unable to merge gvcf files

  Answered 48 views 2 comments 0 points Most recent by bhanuGandham April 26Ask the GATK team
• Example from video (AWS Batch + GATK WDL/Cromwell) does not work for me

  Answered 259 views 6 comments 0 points Most recent by aeahmed April 17Ask the Cromwell + WDL Team
• VCF from RNA-seq data

  Accepted Answer 125 views 10 comments 0 points Most recent by bhanuGandham April 4Ask the GATK team
• Should SplitNCigarReads still be run even though BWA was the aligner used?

  Answered 29 views 1 comment 0 points Most recent by bshifaw April 2Ask the GATK team
• Java FileNotFoundError while executing gatk4

  Accepted Answer 56 views 2 comments 0 points Most recent by lakhujanivijay March 18Ask the GATK team
• SelectVariants Starts Traversal but Does not Progress, High CPU Usage

  Answered 61 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 43 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 27 views 5 comments 0 points Most recent by bhanuGandham January 23Ask the GATK team
• guidelines for BAM realignment in GATK 4

  Accepted Answer 105 views 1 comment 0 points Most recent by bhanuGandham January 7Ask the GATK team
• spark-master is not a recognized option

  Answered 153 views 1 comment 0 points Most recent by bhanuGandham December 2018Ask the GATK team
• about argument presentation

  Answered 43 views 5 comments 0 points Most recent by AdelaideR November 2018Ask the GATK team
• Errors for MuTect2_pon: CalculateContamination

  Answered 96 views 5 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• About java threads in GATK

  Accepted Answer 599 views 10 comments 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• Using GATK pipelines?

  Accepted Answer 22 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 695 views 3 comments 0 points Most recent by shlee October 2018Ask the GATK team
• generate figure from BQSR gatk version 4

  Accepted Answer 211 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 1.1K views 37 comments 0 points Most recent by shlee October 2018Ask the GATK team
• ALT * no deletion

  Accepted Answer 79 views 1 comment 0 points Most recent by shlee October 2018Ask the GATK team
• select intersection, merged VCF files

  Answered 153 views 1 comment 0 points Most recent by shlee October 2018Ask the GATK team
• BQSR -knownSites

  Accepted Answer 155 views 1 comment 0 points Most recent by bhanuGandham September 2018Ask the GATK team
• From one sample to multiple samples

  Accepted Answer 413 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 127 views 6 comments 0 points Most recent by michaelmc September 2018Ask the GATK team
• GATK analysis using Bam files after BWA alignment

  Accepted Answer 87 views 5 comments 0 points Most recent by KateN September 2018Ask the FireCloud Team
• AlleleBalance changes

  Accepted Answer 60 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 119 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 33 views 1 comment 0 points Most recent by Sheila August 2018Ask the GATK team
• Running HaplotypeCaller in GATK

  Accepted Answer 391 views 1 comment 0 points Most recent by Sheila August 2018Ask the GATK team
• Variant Calling

  Accepted Answer 28 views 1 comment 0 points Most recent by dbecker August 2018Ask the GATK team
• the number of reads of diploidy, triploidy and tetraploidy

  Answered 53 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 1.2K 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 227 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 142 views 11 comments 0 points Most recent by Bingley June 2018Ask the FireCloud Team
• "UKNOWN" zygosity in CSV file

  Answered 127 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 4.8K 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 111 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 87 views 1 comment 0 points Most recent by Sheila June 2018Ask the GATK team
• VCF contigs don't match reference genome

  Accepted Answer 164 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 192 views 16 comments 0 points Most recent by Sheila June 2018Ask the GATK team
• Increase marker or point size for PlotDenoisedCopyRatios?

  Accepted Answer 61 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 114 views 2 comments 0 points Most recent by lfall May 2018Ask the GATK team
• BQSR for RNA-seq data

  Accepted Answer 216 views 2 comments 0 points Most recent by lfall May 2018Ask the GATK team
• Let the 2018 GATK workshop season begin!

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

  Answered 206 views 2 comments 0 points Most recent by maierpa April 2018Ask the GATK team
• GATK gradlew bundle Error

  Answered 90 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 40 views 3 comments 0 points Most recent by Sheila April 2018Ask the GATK team
• GATK3.8 vs GATK4 HaplotypeCaller

  Answered 330 views 1 comment 0 points Most recent by Sheila April 2018Ask the GATK team
• no. of cores utilization in haplotypcaller in GVCF mode

  Accepted Answer 620 views 10 comments 1 point Most recent by prasundutta87 March 2018Ask the GATK team
• Truncated Bam error in recalibrated bam file

  Accepted Answer 139 views 7 comments 0 points Most recent by SkyWarrior March 2018Ask the GATK team
• Build Error in Mutect: GATK-Framework

  Answered 79 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• WDL script is not copying the index files for the reference genome from its directory

  Accepted Answer 45 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 91 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 160 views 3 comments 0 points Most recent by shlee March 2018Ask the GATK team
• Not calling all sites in gvcf option (bp_resolution)

  Answered 61 views 1 comment 0 points Most recent by shlee March 2018Ask the GATK team
• DepthOfCoverage fails with java.lang.ArithmeticException: / by zero

  Answered 72 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• Deleting intermediate files

  Answered 664 views 12 comments 0 points Most recent by dinvlad March 2018Ask the Cromwell + WDL Team
• Combine Variants throwing a bug error

  Answered 146 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2018Ask the Cromwell + WDL Team
• CombineGVCFs - All alleles are missing

  Accepted Answer 746 views 9 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• VariantAnnotator is not annotating variants with InbreedingCoeff

  Answered 132 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 118 views 5 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• [Publish] Publish my own WDL including GATK

  Accepted Answer 136 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 57 views 4 comments 0 points Most recent by hjzhou February 2018GenomeSTRiP
• Where to find CreateSequenceDictionary.jar?

  Accepted Answer 2.6K 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 2.5K 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 107 views 1 comment 0 points Most recent by slee January 2018Ask the GATK team
• help with picard CollectHsMetrics

  Answered 186 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 156 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 230 views 3 comments 0 points Most recent by shlee November 2017Ask the GATK team
• Empty file with VariantsToVCF

  Answered 948 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 154 views 1 comment 0 points Most recent by Redmar_van_den_Berg November 2017Ask the GATK team
• bcbio configuration file (bcbio_system.yaml)

  Answered 151 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 116 views 1 comment 0 points Most recent by Sheila October 2017Ask the GATK team
• Mutect 2 java memory shortage: a case study.

  Answered 197 views 1 comment 0 points Most recent by SkyWarrior October 2017Ask the GATK team
• Do you use GATK? Take this survey, win a prize!

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

  Answered 339 views 8 comments 0 points Most recent by Sheila October 2017Ask the GATK team