Ask the WDL team

• Documentation on workspace attributes

  Answered 30 views 2 comments 0 points Most recent by nrashi February 1Ask the FireCloud Team
• Namespace permissions

  Question 28 views 0 comments 0 points Started by nrashi January 31 Ask the FireCloud Team
• Connection attempt to cromwell2.dsde-prod.broadinstitute.org:443 failed

  Answered 51 views 3 comments 0 points Most recent by esalinas February 1Ask the FireCloud Team
• Results discrepancy (very low frequency mutation): GATK vs samtools mpileup (and filtering)

  Answered 74 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 31Ask the GATK team
• Whole Genome Sequencing and structural variation identification in human..

  Question 47 views 0 comments 0 points Started by aneek January 31 GenomeSTRiP
• Navigating to results can be simplified in FireCloud UI

  122 views 15 comments 0 points Most recent by Geraldine_VdAuwera March 1Ask the FireCloud Team
• Whole Genome Sequencing and structural variation identification in human..

  Answered 61 views 2 comments 0 points Most recent by aneek January 31Ask the GATK team
• Firecloud Feature request: Remove old (failed) runs together with their data

  Answered 42 views 2 comments 0 points Most recent by Geraldine_VdAuwera February 8Ask the FireCloud Team
• Task should fail if File output is not known in advance.

  Answered 64 views 5 comments 0 points Most recent by Geraldine_VdAuwera February 1Ask the WDL team
• SNP distribution across chromosome

  Answered 90 views 7 comments 0 points Most recent by Sheila June 14Ask the GATK team
• GATK4: Trouble running "GATK 4 CNV Proportional Coverage for Capture"

  Answered 89 views 2 comments 0 points Most recent by aaronc February 1Ask the GATK team
• DepthOfCoverage takes many hours to run

  Answered 48 views 3 comments 0 points Most recent by Sheila February 3Ask the GATK team
• Redo / Recalculate gvcf bins

  Answered 33 views 1 comment 0 points Most recent by Sheila January 31Ask the GATK team
• CreateSequenceDictionary OutOfMemoryError

  Answered 67 views 1 comment 0 points Most recent by ioantika January 29Ask the GATK team
• GenotypeGVCFs Error:

  Answered 97 views 4 comments 0 points Most recent by Chayan January 29Ask the GATK team
• haplotypecaller new version strand bias

  Answered 41 views 1 comment 0 points Most recent by 2nelly January 27Ask the GATK team
• how to run BaseRecalibrator Queue scripts in parallel

  Answered 106 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 10Ask the GATK team
• java.lang.ExceptionInInitializerError in java.lang.ExceptionInInitializerError

  Answered 642 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 27Ask the GATK team
• Most Variants Called <2.0 Quality of Depth (QD) in VCF files

  Answered 70 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 27Ask the GATK team
• samtools vs picard for gatk analysis

  Answered 77 views 2 comments 0 points Most recent by ibseq January 30Ask the GATK team
• Actual Genomes-in-the-Cloud Docker Container

  Answered 67 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 27Ask the GATK team
• MESSAGE: BUG: requested unknown contig=ERCC-00002 index=-1

  Answered 45 views 2 comments 0 points Most recent by Sheila January 30Ask the GATK team
• seemingly whimsical dbGAP linkage causes workflow failures?

  Answered 46 views 1 comment 0 points Most recent by birger January 26Ask the FireCloud Team
• workflow(WF) running in controlled access(CA) workspace fail if CA turned off during WF execution?

  Answered 47 views 1 comment 0 points Most recent by birger January 26Ask the FireCloud Team
• Annotating vcf with dbSNP IDs: Indel problem

  Answered 52 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 8Ask the GATK team
• dbIndel as input for Mutect2

  Answered 155 views 5 comments 0 points Most recent by escaon January 26Ask the GATK team
• Most efficient way to combine multiple GVCF files

  349 views 3 comments 0 points Most recent by Geraldine_VdAuwera February 9Ask the GATK team
• Does HaplotypeCaller block the bam and/or reference while it is running?

  Answered 75 views 2 comments 0 points Most recent by AnaK January 27Ask the GATK team
• empty error?

  Answered 44 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 26Ask the FireCloud Team
• GATK HaplotypeCaller Error: Java stack error

  Answered 100 views 2 comments 0 points Most recent by gracec January 28Ask the GATK team
• Detection of somatic mutations with RNAseq - Mutect2

  Answered 152 views 2 comments 0 points Most recent by mcharles February 2Ask the GATK team
• Which one should I use for ContEst --popFile?

  Answered 462 views 22 comments 0 points Most recent by shlee February 21Ask the GATK team
• call caching error with softlink output files

  Answered 63 views 3 comments 0 points Most recent by Redmar_van_den_Berg February 20Ask the WDL team
• Picard Sort Vcf Error

  Answered 138 views 3 comments 0 points Most recent by Geraldine_VdAuwera February 3Ask the GATK team
• Cannot access controlled access workspaces on FireCloud

  Answered 209 views 35 comments 0 points Most recent by birger February 14Ask the FireCloud Team
• sample set size viewing (in?)ability

  Answered 85 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 26Ask the FireCloud Team
• What does "Input evaluation for Call failed.\nNo coercion defined from " Mean

  Answered 44 views 1 comment 0 points Most recent by KateN January 24Ask the WDL team
• Exception when processing alignment for BAM index

  Answered 161 views 8 comments 0 points Most recent by Geraldine_VdAuwera January 27Ask the GATK team
• VariantFiltration error

  Answered 51 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 24Ask the GATK team
• Variant recalibration (WQSR) after pooled calling

  113 views 8 comments 0 points Most recent by Geraldine_VdAuwera January 27Ask the GATK team
• Is there an updated MutationCalling_Mutect_v1-2_BETA_cfg?

  Answered 35 views 5 comments 0 points Most recent by esalinas January 24Ask the FireCloud Team
• Support team appreciation day -- say hi and get a prize

  225 views 16 comments 0 points Most recent by wisonlee April 12Announcements
• FireCloud Cromwell incorrectly instructing JES to run task on preemptible VM

  Answered 150 views 16 comments 0 points Most recent by Geraldine_VdAuwera January 26Ask the FireCloud Team
• Output active regions in GATK4 HaplotypeCaller

  Answered 55 views 1 comment 0 points Most recent by shlee January 24Ask the GATK team
• Format of gatk4cnv_padded_target_bed_capture in "GATK 4 CNV Proportional Coverage for Capture"

  Answered 75 views 2 comments 0 points Most recent by LeeTL1220 January 24Ask the GATK team
• Resume pipeline

  Answered 140 views 6 comments 0 points Most recent by Geraldine_VdAuwera April 13Ask the WDL team
• Task with variable as output?

  Answered 49 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 23Ask the WDL team
• Why am I seeing no evidence of preemption?

  Answered 39 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 23Ask the FireCloud Team
• google JES/backend running but not running? is it running or not?

  Answered 76 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 23Ask the FireCloud Team
• MergeBamAlignment Fails, can use AddOrReplaceReadGroups to debug?

  Answered 87 views 1 comment 0 points Most recent by shlee January 24Ask the GATK team
• Haplotype Caller Error: Graph must have ref source and sink vertices

  Answered 42 views 3 comments 0 points Most recent by Sheila January 24Ask the GATK team
• How to obtain a GATK commercial license?

  Answered 56 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 23Ask the GATK team
• Error details: The contig order in variant and reference is not the same after running SortVCF

  Answered 66 views 2 comments 0 points Most recent by astridboehne January 24Ask the GATK team
• What is the size of the internal window used by gatk haplotypecaller's sliding window approach?

  Answered 66 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 24Ask the GATK team
• "File not found" errors when using call caching

  Answered 79 views 3 comments 0 points Most recent by KateVoss January 30Ask the WDL team
• v3.7-0-gcfedb67: -T RealignerTargetCreator does not support --known blah.vcf.gz

  Answered 134 views 10 comments 0 points Most recent by mglclinical April 19Ask the GATK team
• about running variant calling ( final UnifiedGenotyper and HaplotypeCaller vcf files )

  Answered 37 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 21Ask the GATK team
• MuTect2 Output -- How can this be somatic mutation

  Answered 106 views 8 comments 0 points Most recent by Sheila February 6Ask the GATK team
• Not to generate final svdiscovery.dels.vcf

  Answered 66 views 1 comment 0 points Most recent by bhandsaker January 23GenomeSTRiP
• DP field Mutect2

  97 views 3 comments 0 points Most recent by Sheila February 1Ask the GATK team
• Data with newlines and tabs

  Answered 90 views 9 comments 0 points Most recent by yfarjoun January 27Ask the FireCloud Team
• Mutect2 ERROR: Null qss lines in bcbio log

  Answered 58 views 1 comment 0 points Most recent by Sheila January 23Ask the GATK team
• When myfile.vcf.gz is myfile.vcf on command line?

  Answered 64 views 5 comments 0 points Most recent by KateN January 20Ask the WDL team
• How can a method configuration locate a file generated by WDL method ${write_lines(Array[File])}?

  Question 331 views 18 comments 0 points Most recent by gordon123 March 23Ask the FireCloud Team
• Firecloud UI error messages

  Answered 41 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 19Ask the FireCloud Team
• IndelRealigner

  Answered 81 views 2 comments 0 points Most recent by Geraldine_VdAuwera January 21Ask the GATK team
• CatVariants Error - Features added out of order

  Answered 50 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 21Ask the GATK team
• Missing positions after GenotypeGVCFs

  Answered 160 views 14 comments 0 points Most recent by Sheila January 27Ask the GATK team
• missing error message for workflows? missing from workflow log? missing from UI?

  Answered 48 views 2 comments 0 points Most recent by esalinas January 19Ask the FireCloud Team
• error CombineVariants UNIQUIFY

  Answered 84 views 2 comments 0 points Most recent by pachchek January 25Ask the GATK team
• Gradle test failed after building GATK 4 Alpha

  Answered 65 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 18Ask the GATK team
• How can I prevent the file header from showing up in gigantic font?

  263 views 1 comment 0 points Most recent by shlee January 18Ask the GATK team
• CombineVariants --variants : can I give both a variant name and a file type?

  Answered 110 views 4 comments 0 points Most recent by JocelynSP January 19Ask the GATK team
• How can I find the version of MuTect2 in broadinstitute_cga/MutationCalling_Mutect_v1-2_BETA_cfg?

  Answered 106 views 8 comments 0 points Most recent by esalinas January 20Ask the FireCloud Team
• Annotation is lost when merging GVCF files with GenotypeGVCFs

  62 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 17Ask the GATK team
• GATK 3.6 api: GATK cannot find my Walker when I use a java lambda / Filter ?

  Answered 55 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 17Ask the GATK team
• Custom Walker :

  Answered 63 views 2 comments 0 points Most recent by Geraldine_VdAuwera January 17Ask the GATK team
• call-caching not working?

  Answered 77 views 3 comments 0 points Most recent by Redmar_van_den_Berg January 22Ask the WDL team
• ERROR running SplitNCigarReads on RNAseq data using Ensembl Mus Musculus referece FASTA file

  Answered 71 views 5 comments 0 points Most recent by Sheila February 27Ask the GATK team
• SPlitNCigarReads: endless memory hunger

  Answered 171 views 10 comments 0 points Most recent by shlee January 27Ask the GATK team
• GenotypeGVCF crashes ?

  Answered 61 views 1 comment 0 points Most recent by Sheila January 18Ask the GATK team
• SubWorkflow / SubTask / Task encapsulation

  Answered 84 views 2 comments 0 points Most recent by EADG January 17Ask the WDL team
• Full bash autocompletion for wdltool

  Answered 35 views 1 comment 0 points Most recent by KateN January 17Ask the WDL team
• VQSR - ./. genotypes retained after VQSR filtering

  72 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 17Ask the GATK team
• WDL: best way to tell when a task with no output is done?

  Answered 45 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 17Ask the WDL team
• Questions about BQSR (2014-2016)

  413 views 82 comments 0 points Most recent by Geraldine_VdAuwera December 2016Ask the GATK team
• [E::bwa_idx_load_from_disk] fail to locate the index files

  Answered 258 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 17Ask the GATK team
• Old version of GATK

  Answered 46 views 2 comments 0 points Most recent by Sheila January 17Ask the GATK team
• Error with SamTools in GATK 4 CNV Proportional Coverage

  Answered 53 views 1 comment 0 points Most recent by Sheila January 17Ask the GATK team
• multiple fastq files for a sample produced same number of columns in vcf, how can we produce one?

  Answered 47 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 13Ask the GATK team
• Duplicate samples in a sample set

  Answered 63 views 4 comments 0 points Most recent by yfarjoun February 8Ask the FireCloud Team
• GATK4 Plot segmented coverage

  Answered 174 views 11 comments 0 points Most recent by shlee February 3Ask the GATK team
• How can I tell if my jobs were preempted?

  Answered 77 views 3 comments 0 points Most recent by Geraldine_VdAuwera January 23Ask the FireCloud Team
• How to compare two vcf files of two cultivars?

  Answered 289 views 7 comments 0 points Most recent by shis January 30Ask the GATK team
• Phasing

  Answered 56 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 20Ask the GATK team
• Inconsistencies with color-coding in workflow timing diagram

  Answered 47 views 2 comments 0 points Most recent by jneff January 13Ask the FireCloud Team
• Can you provide a detailed explanation of workflow timing diagram?

  Answered 69 views 5 comments 0 points Most recent by birger January 18Ask the FireCloud Team
• I need help. GATK Haplotypecaller says my dict is empty but it isn't??

  Answered 202 views 13 comments 0 points Most recent by Sheila March 1Ask the GATK team
• Project i-dotting and t-crossing

  27 views 1 comment 0 points Most recent by jneff January 12Ask the FireCloud Team
• Picard Optical Duplicates calculation 2.0 vs 2.1+

  Answered 50 views 1 comment 0 points Most recent by shlee January 17Ask the GATK team