gatk

Discussion List

• HaplotypeCallerSpark throws error Unable to find class: htsjdk.samtools.reference.AbstractFastaSeque

  Answered 107 views 9 comments 0 points Most recent by LouisB December 2019Ask the GATK team
• BI and BD Default Quality Scores?

  Answered 23 views 1 comment 0 points Most recent by bhanuGandham December 2019Ask the GATK team
• Download small_exac_common_3_grch38.vcf.gz file

  Answered 124 views 1 comment 0 points Most recent by bhanuGandham November 2019Ask the GATK team
• How to identify duplicated genes in VCF file obtained after GATK pipeline?

  Answered 19 views 1 comment 0 points Most recent by bhanuGandham November 2019Ask the GATK team
• BAM file generated by GATK HaplotypeCaller shows duplicates, not fixed by Picard FixMateInformation

  Answered 69 views 6 comments 0 points Most recent by elcortegano November 2019Ask the GATK team
• GATK-Mutect2 Running and Output Error in Terra

  Answered 35 views 1 comment 0 points Most recent by bhanuGandham October 2019Ask the GATK team
• GATK_docker image to run Mutect2

  Accepted Answer 47 views 6 comments 0 points Most recent by Tiffany_at_Broad October 2019Ask the GATK team
• Funcotator timing expectations

  Accepted Answer 46 views 4 comments 0 points Most recent by bhanuGandham September 2019Ask the GATK team
• AddOrReplaceReadGroups error even when all details are provided

  Answered 100 views 2 comments 0 points Most recent by bhanuGandham September 2019Ask the GATK team
• Alternative resources for Mutect2/GetPileupSummaries when dealing with genome data

  Answered 84 views 3 comments 0 points Most recent by akovalsk September 2019Ask the GATK team
• Setting a specific seed when using GATK

  Accepted Answer 54 views 3 comments 0 points Most recent by bhanuGandham August 2019Ask the GATK team
• Different resource for Mutect2/GetPileupSummaries when dealing with genome data

  29 views 0 comments 0 points Started by michaelmc August 2019 Zoo & Garden
• Using GATK SelectVariants to filter based on calculated allele frequency

  Answered 304 views 4 comments 0 points Most recent by bhanuGandham August 2019Ask the GATK team
• How do MuTect1.1.4 and MuTect2 differ in Tumor only mode (no matched control) variant calling

  Answered 88 views 1 comment 0 points Most recent by davidben August 2019Ask the GATK team
• GATK - HaplotypeCaller is so slow, is this normal??

  Accepted Answer 2K views 11 comments 0 points Most recent by lakhujanivijay July 2019Ask the GATK team
• GATK 4.1.0.0 Release

  1.4K views 9 comments 0 points Most recent by bhanuGandham July 2019Announcements
• VQSR filtering and dbSNP

  Answered 186 views 2 comments 0 points Most recent by jush July 2019Ask the GATK team
• Piped command for realignment of BAM files

  Question 79 views 1 comment 0 points Most recent by bshifaw July 2019Ask the GATK team
• why variant callers's (GATK3.8 and GATK 4.0) results are different ?

  Question 32 views 0 comments 0 points Started by Shariq June 2019 Ask the GATK team
• GATK variant calling

  Answered 169 views 11 comments 0 points Most recent by bshifaw June 2019Ask the GATK team
• Variant filtration by allelic balance bias

  Answered 101 views 1 comment 0 points Most recent by bhanuGandham June 2019Ask the GATK team
• VariantFiltration: how to filter samples where less then 95% of reads agree with the called genotype

  Accepted Answer 611 views 4 comments 0 points Most recent by Nolan_Shelley June 2019Ask the GATK team
• Error with GenomicsDBImport input file

  Accepted Answer 39 views 1 comment 0 points Most recent by nparmalee June 2019Ask the GATK team
• SelectVariants - java.lang.IllegalStateException: Allele in genotype not in the variant context

  Answered 111 views 2 comments 0 points Most recent by mpmachado June 2019Ask the GATK team
• AD allele depth interpretation

  Answered 314 views 1 comment 0 points Most recent by Amir_Ariff June 2019Ask the GATK team
• Invalid SAM?

  Answered 257 views 3 comments 0 points Most recent by AdelaideR May 2019Ask the GATK team
• MergeBamAlignment warning in the best practice pipeline

  Accepted Answer 224 views 5 comments 0 points Most recent by AdelaideR May 2019Ask the GATK team
• Picard AddOrReplaceGroups for singly biological sample

  Accepted Answer 65 views 5 comments 0 points Most recent by bshifaw May 2019Ask the GATK team
• Mapping a locus to a chromosome in a genome

  Answered 18 views 1 comment 0 points Most recent by bhanuGandham May 2019Ask the GATK team
• GATK IndelRealigner error: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated

  Answered 154 views 1 comment 0 points Most recent by bshifaw May 2019Ask the GATK team
• Standard practice for VCF filtering for the purpose of fingerprinting via proportion IBS?

  Answered 328 views 11 comments 0 points Most recent by golharam April 2019Ask the GATK team
• Unable to merge gvcf files

  Answered 76 views 2 comments 0 points Most recent by bhanuGandham April 2019Ask the GATK team
• Example from video (AWS Batch + GATK WDL/Cromwell) does not work for me

  Answered 393 views 6 comments 0 points Most recent by aeahmed April 2019Ask the Cromwell + WDL Team
• VCF from RNA-seq data

  Accepted Answer 406 views 10 comments 0 points Most recent by bhanuGandham April 2019Ask the GATK team
• Should SplitNCigarReads still be run even though BWA was the aligner used?

  Answered 36 views 1 comment 0 points Most recent by bshifaw April 2019Ask the GATK team
• Java FileNotFoundError while executing gatk4

  Accepted Answer 125 views 2 comments 0 points Most recent by lakhujanivijay March 2019Ask the GATK team
• SelectVariants Starts Traversal but Does not Progress, High CPU Usage

  Answered 81 views 9 comments 0 points Most recent by AdelaideR February 2019Ask the GATK team
• How to output AD ref and alt in separate columns with VariantsToTable

  Accepted Answer 71 views 5 comments 0 points Most recent by steve1 February 2019Ask the GATK team
• IntervalListTools UNION corner case: doesn't keep all name fields if merged coordinates are same

  Answered 31 views 5 comments 0 points Most recent by bhanuGandham January 2019Ask the GATK team
• guidelines for BAM realignment in GATK 4

  Accepted Answer 133 views 1 comment 0 points Most recent by bhanuGandham January 2019Ask the GATK team
• spark-master is not a recognized option

  Answered 276 views 1 comment 0 points Most recent by bhanuGandham December 2018Ask the GATK team
• about argument presentation

  Answered 46 views 5 comments 0 points Most recent by AdelaideR November 2018Ask the GATK team
• Errors for MuTect2_pon: CalculateContamination

  Answered 108 views 5 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• About java threads in GATK

  Accepted Answer 985 views 10 comments 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• Using GATK pipelines?

  Accepted Answer 27 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 1K views 3 comments 0 points Most recent by shlee October 2018Ask the GATK team
• generate figure from BQSR gatk version 4

  Accepted Answer 290 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 1.3K views 37 comments 0 points Most recent by shlee October 2018Ask the GATK team
• ALT * no deletion

  Accepted Answer 130 views 1 comment 0 points Most recent by shlee October 2018Ask the GATK team
• select intersection, merged VCF files

  Answered 240 views 1 comment 0 points Most recent by shlee October 2018Ask the GATK team
• BQSR -knownSites

  Accepted Answer 277 views 1 comment 0 points Most recent by bhanuGandham September 2018Ask the GATK team
• From one sample to multiple samples

  Accepted Answer 539 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 257 views 6 comments 0 points Most recent by michaelmc September 2018Ask the GATK team
• GATK analysis using Bam files after BWA alignment

  Accepted Answer 98 views 5 comments 0 points Most recent by KateN September 2018Ask the FireCloud Team
• AlleleBalance changes

  Accepted Answer 95 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 195 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 54 views 1 comment 0 points Most recent by Sheila August 2018Ask the GATK team
• Running HaplotypeCaller in GATK

  Accepted Answer 526 views 1 comment 0 points Most recent by Sheila August 2018Ask the GATK team
• Variant Calling

  Accepted Answer 32 views 1 comment 0 points Most recent by dbecker August 2018Ask the GATK team
• the number of reads of diploidy, triploidy and tetraploidy

  Answered 75 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 1.4K 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 320 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 175 views 11 comments 0 points Most recent by Bingley June 2018Ask the FireCloud Team
• "UKNOWN" zygosity in CSV file

  Answered 142 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 4.9K 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 137 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 118 views 1 comment 0 points Most recent by Sheila June 2018Ask the GATK team
• VCF contigs don't match reference genome

  Accepted Answer 282 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 264 views 16 comments 0 points Most recent by Sheila June 2018Ask the GATK team
• Increase marker or point size for PlotDenoisedCopyRatios?

  Accepted Answer 82 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 146 views 2 comments 0 points Most recent by lfall May 2018Ask the GATK team
• BQSR for RNA-seq data

  Accepted Answer 346 views 2 comments 0 points Most recent by lfall May 2018Ask the GATK team
• Let the 2018 GATK workshop season begin!

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

  Answered 250 views 2 comments 0 points Most recent by maierpa April 2018Ask the GATK team
• GATK gradlew bundle Error

  Answered 131 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 44 views 3 comments 0 points Most recent by Sheila April 2018Ask the GATK team
• GATK3.8 vs GATK4 HaplotypeCaller

  Answered 499 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 943 views 10 comments 1 point Most recent by prasundutta87 March 2018Ask the GATK team
• Truncated Bam error in recalibrated bam file

  Accepted Answer 230 views 7 comments 0 points Most recent by SkyWarrior March 2018Ask the GATK team
• Build Error in Mutect: GATK-Framework

  Answered 99 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 59 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 149 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 216 views 3 comments 0 points Most recent by shlee March 2018Ask the GATK team
• Not calling all sites in gvcf option (bp_resolution)

  Answered 71 views 1 comment 0 points Most recent by shlee March 2018Ask the GATK team
• DepthOfCoverage fails with java.lang.ArithmeticException: / by zero

  Answered 92 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• Deleting intermediate files

  Answered 881 views 12 comments 0 points Most recent by dinvlad March 2018Ask the Cromwell + WDL Team
• Combine Variants throwing a bug error

  Answered 180 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2018Ask the Cromwell + WDL Team
• CombineGVCFs - All alleles are missing

  Accepted Answer 839 views 9 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• VariantAnnotator is not annotating variants with InbreedingCoeff

  Answered 153 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 188 views 5 comments 0 points Most recent by Sheila February 2018Ask the GATK team
• [Publish] Publish my own WDL including GATK

  Accepted Answer 142 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 72 views 4 comments 0 points Most recent by hjzhou February 2018GenomeSTRiP
• Where to find CreateSequenceDictionary.jar?

  Accepted Answer 3.9K 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 2.6K 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 121 views 1 comment 0 points Most recent by slee January 2018Ask the GATK team
• help with picard CollectHsMetrics

  Answered 267 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 174 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 357 views 3 comments 0 points Most recent by shlee November 2017Ask the GATK team
• Empty file with VariantsToVCF

  Answered 974 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 208 views 1 comment 0 points Most recent by Redmar_van_den_Berg November 2017Ask the GATK team