depthofcoverage

Discussion List

• GATK4 does not include DepthOfCoverage tool

  1.3K views 17 comments 0 points Most recent by bhanuGandham June 20Ask the GATK team
• Depth of coverage in GATK 4

  1.8K views 5 comments 0 points Most recent by maricom June 1Ask the GATK team
• DepthOfCoverage in parallel mode does not actually run in parallel

  Accepted Answer 89 views 6 comments 0 points Most recent by bhanuGandham April 12Ask the GATK team
• Analysis Pipeline Discrepancy in SNP Calling and Coverage

  Answered 63 views 3 comments 0 points Most recent by AdelaideR February 5Ask the GATK team
• Infuence of Coverage Depth Difference in Tumor & Normal Sequencing Data in Somatic Mutation Calling

  Answered 113 views 1 comment 0 points Most recent by AdelaideR December 2018Ask the GATK team
• Same pipeline for exome seq variant calling with different results

  47 views 1 comment 0 points Most recent by bhanuGandham November 2018Ask the GATK team
• Using depth of coverage metrics for variant evaluation

  2.8K views 13 comments 1 point Most recent by tytolin October 2018Methods and Algorithms
• Coverage after Base Quality Recalibration: enough for variant calling?

  Accepted Answer 114 views 3 comments 0 points Most recent by Geraldine_VdAuwera October 2018Ask the GATK team
• How to generate RefSeq ROD

  Accepted Answer 2.3K views 10 comments 0 points Most recent by shlee August 2018Ask the GATK team
• How to calculate minReadsAtLocus

  Answered 31 views 1 comment 0 points Most recent by Sheila July 2018Ask the GATK team
• Depth with and without Soft-Clipping

  Answered 140 views 3 comments 0 points Most recent by Sheila May 2018Ask the GATK team
• DepthOfCoverage

  Accepted Answer 263 views 1 comment 0 points Most recent by Sheila May 2018Ask the GATK team
• In which step exactly the allele depth / frequency is used during variant calling?

  Accepted Answer 53 views 1 comment 0 points Most recent by Sheila April 2018Ask the GATK team
• Can GATK accepts more than one bed file while computing depth of coverage?

  Answered 75 views 3 comments 0 points Most recent by shlee March 2018Ask the GATK team
• DepthOfCoverage fails with java.lang.ArithmeticException: / by zero

  Answered 65 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• What is the significance of "Depth across all samples" (DP) in INFO ?

  Accepted Answer 661 views 8 comments 0 points Most recent by Sheila December 2017Ask the GATK team
• Abnormally high per-sample depth after running GenotypeGVCFs

  Answered 46 views 1 comment 0 points Most recent by Sheila November 2017Ask the GATK team
• Different coverage metrics between GATK and PICARD

  Answered 567 views 5 comments 0 points Most recent by asaki November 2017Ask the GATK team
• GATK depth of coverage

  Answered 1K views 1 comment 0 points Most recent by SkyWarrior October 2017Ask the GATK team
• HC listing depth one read less

  Answered 176 views 18 comments 0 points Most recent by Sheila October 2017Ask the GATK team
• DP differences between haploid and diploid mode

  Answered 364 views 9 comments 0 points Most recent by Sheila October 2017Ask the GATK team
• Not enough memory for depth of Coverage as single thread

  Accepted Answer 155 views 1 comment 0 points Most recent by EADG September 2017Ask the GATK team
• DepthOfCoverage in v4

  Answered 86 views 1 comment 0 points Most recent by Sheila August 2017Ask the GATK team
• can depth of bam file at some position is lower than depth of vcf?

  Answered 111 views 2 comments 0 points Most recent by mankyua August 2017Ask the GATK team
• CalculateTargetCoverage error

  Answered 337 views 3 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• How to return an Array given as input

  Accepted Answer 245 views 2 comments 0 points Most recent by dbecker July 2017Ask the Cromwell + WDL Team
• What does the output of DepthOfCoverage means?

  Answered 3.4K views 5 comments 0 points Most recent by Sheila May 2017Ask the GATK team
• depth of coverage from gVCF files

  Accepted Answer 1.1K views 5 comments 0 points Most recent by Sheila May 2017Ask the GATK team
• GATK DepthOfCoverage

  Accepted Answer 589 views 2 comments 1 point Most recent by vesna_pajic April 2017Ask the GATK team
• Should I use sorted.bam or clean_dedup_recalibrated.bam for getting the metrics using Picard?

  Accepted Answer 117 views 2 comments 0 points Most recent by Nanda April 2017Ask the GATK team
• Allele frequency and depth VCF produced by MuTect2

  Answered 697 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2017Ask the GATK team
• Extremely high depth of coverage

  424 views 4 comments 0 points Most recent by adri_somavilla February 2017Ask the GATK team
• DepthOfCoverage takes many hours to run

  Answered 142 views 3 comments 0 points Most recent by Sheila February 2017Ask the GATK team
• Downsampling Experiment

  Accepted Answer 1.1K views 8 comments 0 points Most recent by Geraldine_VdAuwera December 2016Ask the GATK team
• depthofcoverage: How does depthofcoverage treat reads with SAM flag value 0?

  Answered 148 views 1 comment 0 points Most recent by Sheila October 2016Ask the GATK team
• Bug report: DepthOfCoverage csv output

  Answered 136 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• DepthOfCoverage multiple samples

  Accepted Answer 433 views 4 comments 0 points Most recent by adri_somavilla August 2016Ask the GATK team
• Error in DepthOfCoverage for interval of 1bp

  Accepted Answer 172 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2016Ask the GATK team
• DepthOfCoverage Genelist Error

  Answered 148 views 1 comment 0 points Most recent by Geraldine_VdAuwera June 2016Ask the GATK team
• interpreting depth of coverage

  Accepted Answer 341 views 1 comment 0 points Most recent by Sheila May 2016Ask the GATK team
• DepthOfCoverage -genelist: 'total coverage' and 'mean coverage' explanation

  Accepted Answer 435 views 0 comments 0 points Started by user31888 April 2016 Ask the GATK team
• GATK depthofcoverage runtimeerror: nullpointerexception

  Accepted Answer 430 views 7 comments 0 points Most recent by Sheila April 2016Ask the GATK team
• Depth of Coverage doesn't factor Y chromosome genomic repetitive sequences?

  Accepted Answer 585 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2016Ask the GATK team
• DepthOfCoverage run time 4.6 days?

  Answered 270 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2016Ask the GATK team
• Discrepancy between GATK DepthOfCoverage and samtools mpileup - depth values

  Answered 315 views 1 comment 0 points Most recent by Sheila February 2016Ask the GATK team
• Error in calculaitng DepthOfCoverage for a single BAM file

  Accepted Answer 306 views 2 comments 0 points Most recent by aditisk February 2016Ask the GATK team
• determining read depth from bam file: 4 methods, 3 different results

  Accepted Answer 1.7K views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• maxReadsForRealignment value and depthofcoverage results don't jibe; indelrealigner

  Accepted Answer 264 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2015Ask the GATK team
• RE: Gene list headers

  Accepted Answer 1K views 3 comments 0 points Most recent by marlaux November 2015Ask the GATK team
• DepthOfCoverage memory usage

  Accepted Answer 527 views 6 comments 0 points Most recent by igor November 2015Ask the GATK team
• DepthOfCoverage missing to report some locations

  Answered 156 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015Ask the GATK team
• Haplotype Caller on SOLID samples reports less coverage per variant compared to --bamoutput

  Accepted Answer 316 views 5 comments 0 points Most recent by wariobrega August 2015Ask the GATK team
• How to calulate base counts percentage?

  223 views 1 comment 0 points Most recent by Sheila July 2015Ask the GATK team
• Problem in calculating Depth of Coverage using GenomeAnalysisTK.jar

  Answered 1.7K views 8 comments 0 points Most recent by Sheila July 2015Ask the GATK team
• disable NotPrimaryAlignmentFilter in DepthOfCoverage

  Answered 302 views 3 comments 0 points Most recent by Sheila July 2015Ask the GATK team
• Odd distribution of Coverage for GATK HaplotypeCaller Variants

  Answered 1.5K views 21 comments 0 points Most recent by Geraldine_VdAuwera July 2015Ask the GATK team
• DepthOfCoverage and DiagnoseTargets: our plans for development and support

  2.3K views 9 comments 0 points Most recent by Geraldine_VdAuwera June 2015Announcements
• DepthOfCoverage, QualifyMissingIntervals and DiagnoseTargets?

  Answered 428 views 4 comments 0 points Most recent by Blue May 2015Ask the GATK team
• variant detection: DP and Mendelization

  Accepted Answer 239 views 1 comment 0 points Most recent by Sheila May 2015Ask the GATK team
• Coverage per gene by Exons intervals hg19

  Accepted Answer 1.1K views 2 comments 0 points Most recent by mariagr April 2015Ask the GATK team
• How does DepthofCoverage treat half-mapped reads?

  Accepted Answer 191 views 1 comment 0 points Most recent by Geraldine_VdAuwera March 2015Ask the GATK team
• which file to use as input to DepthOfCoverage?

  Answered 319 views 5 comments 0 points Most recent by Geraldine_VdAuwera March 2015Ask the GATK team
• % Depth at X vs cumulative_coverage_proportions

  Answered 232 views 1 comment 0 points Most recent by Sheila December 2014Ask the GATK team
• DepthOfCoverage summary reports too many bases

  Answered 2K views 41 comments 0 points Most recent by JamesM December 2014Ask the GATK team
• HaplotypeCaller: --min_base_quality_score vs -stand_call_conf and -stand_emit_conf flags

  Accepted Answer 2.6K views 2 comments 0 points Most recent by gwilymh December 2014Ask the GATK team
• DepthOfCoverage interval_summary and interval_statistics

  Accepted Answer 798 views 4 comments 0 points Most recent by Geraldine_VdAuwera December 2014Ask the GATK team
• DepthOfCoverage interval_summary +1 on the start position of each intervals

  Accepted Answer 449 views 4 comments 0 points Most recent by Geraldine_VdAuwera December 2014Ask the GATK team
• DepthOfCoverage error

  Answered 164 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2014Ask the GATK team
• DepthOfCoverage: ERROR MESSAGE: Error parsing line at byte position

  Accepted Answer 1.8K views 3 comments 0 points Most recent by Sheila November 2014Ask the GATK team
• Getting insertion counts

  Accepted Answer 698 views 8 comments 0 points Most recent by Geraldine_VdAuwera November 2014Ask the GATK team
• DepthofCoverage: More rows in output that in target file

  Accepted Answer 290 views 2 comments 0 points Most recent by mehar November 2014Ask the GATK team
• Exon output Depth of Coverage

  Accepted Answer 1.9K views 4 comments 0 points Most recent by mehar November 2014Ask the GATK team
• DepthofCoverage, argument with name 'includeRefNSites' isn't defined?

  Accepted Answer 405 views 6 comments 0 points Most recent by stevenlovesscience November 2014Ask the GATK team
• DepthOfCoverage only analyzing one gene of two overlapping genes

  Accepted Answer 239 views 2 comments 0 points Most recent by cparobek October 2014Ask the GATK team
• DepthOfCoverage calculateCoverageOverGenes missing genes

  Answered 494 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2014Ask the GATK team
• Problem due to: "MESSAGE: Input files reads and reference have incompatible contigs"

  Accepted Answer 2.2K views 7 comments 0 points Most recent by Geraldine_VdAuwera September 2014Ask the GATK team
• depth of coverage link

  Accepted Answer 721 views 5 comments 0 points Most recent by estif74 July 2014Ask the GATK team
• Feature Request: Parallelize more GATK tools

  Accepted Answer 292 views 2 comments 0 points Most recent by bredeson June 2014Ask the GATK team
• Minimum depth requirement when creating gVCFs files?

  Accepted Answer 775 views 8 comments 0 points Most recent by Geraldine_VdAuwera May 2014Ask the GATK team
• Depth of Coverage - Only one type of output

  Answered 2.1K views 8 comments 0 points Most recent by Geraldine_VdAuwera April 2014Ask the GATK team
• memory used by DepthOfCoverage

  Accepted Answer 1.3K views 3 comments 0 points Most recent by chunxuan March 2014Ask the GATK team
• BaseCoverageDistribution

  Accepted Answer 820 views 8 comments 0 points Most recent by avidLearner January 2014Ask the GATK team
• Is the parallelism documentation for DepthOfCoverage correct?

  Answered 658 views 8 comments 0 points Most recent by Shrey_S January 2014Ask the GATK team
• how does the tools DepthOfCoverage work?

  393 views 4 comments 0 points Most recent by ahda December 2013Ask the GATK team
• Cosideration of secondary alignments and duplicates in DepthOfCoverage?

  Accepted Answer 320 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2013Ask the GATK team
• DepthofCoverage

  Answered 519 views 3 comments 0 points Most recent by pdexheimer November 2013Ask the GATK team
• DepthOfCoverage for whole genome: skipped few regions

  Accepted Answer 554 views 5 comments 0 points Most recent by Geraldine_VdAuwera October 2013Ask the GATK team
• DepthOfCoverage

  Accepted Answer 643 views 7 comments 0 points Most recent by Geraldine_VdAuwera October 2013Ask the GATK team
• DepthOfCoverage (without -L option) output

  Accepted Answer 968 views 5 comments 0 points Most recent by Geraldine_VdAuwera October 2013Ask the GATK team
• DepthOfCoverage gene list Ensembl format

  Answered 893 views 1 comment 0 points Most recent by Geraldine_VdAuwera September 2013Ask the GATK team
• DepthOfCoverage multi-threading

  Accepted Answer 1K views 2 comments 0 points Most recent by tommycarstensen September 2013Ask the GATK team
• DP and chromosome filtering

  Accepted Answer 382 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2013Ask the GATK team
• DepthofCoverage Walker

  Accepted Answer 540 views 5 comments 0 points Most recent by pmudvari June 2013Ask the GATK team
• Undocumented change in 2.4? (-A DepthOfCoverage)

  Accepted Answer 921 views 11 comments 1 point Most recent by Carneiro May 2013Ask the GATK team
• bam is malformed depthofcoverage

  Answered 1.6K views 3 comments 0 points Most recent by remimaglione May 2013Ask the GATK team
• DepthOfCoverage producing "extremely high quality score" error

  Accepted Answer 1.9K views 12 comments 0 points Most recent by Carneiro May 2013Ask the GATK team
• Depth of Coverage - reported only first exon

  Answered 474 views 4 comments 0 points Most recent by MarcelaD May 2013Ask the GATK team
• how to solve a problem with the depthofcoverage input format?

  Answered 307 views 2 comments 0 points Most recent by ge2sasag April 2013Ask the GATK team
• Concerns regarding transition from DepthOfCoverage to DiagnoseTargets.

  Accepted Answer 378 views 1 comment 0 points Most recent by Geraldine_VdAuwera March 2013Ask the GATK team
• Remove duplicate reads from the DepthOfCoverage

  Answered 1.8K views 3 comments 0 points Most recent by Geraldine_VdAuwera January 2013Ask the GATK team