depthofcoverage

Discussion List

• GATK4 does not include DepthOfCoverage tool

  957 views 12 comments 0 points Most recent by FPBarthel February 12Ask the GATK team
• Analysis Pipeline Discrepancy in SNP Calling and Coverage

  Answered 30 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 61 views 1 comment 0 points Most recent by AdelaideR December 2018Ask the GATK team
• Same pipeline for exome seq variant calling with different results

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

  2.6K views 13 comments 1 point Most recent by tytolin October 2018Methods and Algorithms
• Coverage after Base Quality Recalibration: enough for variant calling?

  Accepted Answer 80 views 3 comments 0 points Most recent by Geraldine_VdAuwera October 2018Ask the GATK team
• How to generate RefSeq ROD

  Accepted Answer 2.2K views 10 comments 0 points Most recent by shlee August 2018Ask the GATK team
• How to calculate minReadsAtLocus

  Answered 20 views 1 comment 0 points Most recent by Sheila July 2018Ask the GATK team
• Depth with and without Soft-Clipping

  Answered 88 views 3 comments 0 points Most recent by Sheila May 2018Ask the GATK team
• DepthOfCoverage

  Accepted Answer 185 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 43 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 53 views 3 comments 0 points Most recent by shlee March 2018Ask the GATK team
• DepthOfCoverage fails with java.lang.ArithmeticException: / by zero

  Answered 51 views 1 comment 0 points Most recent by Sheila March 2018Ask the GATK team
• Depth of coverage in GATK 4

  1K views 2 comments 0 points Most recent by scottfrod March 2018Ask the GATK team
• What is the significance of "Depth across all samples" (DP) in INFO ?

  Accepted Answer 545 views 8 comments 0 points Most recent by Sheila December 2017Ask the GATK team
• Abnormally high per-sample depth after running GenotypeGVCFs

  Answered 42 views 1 comment 0 points Most recent by Sheila November 2017Ask the GATK team
• Different coverage metrics between GATK and PICARD

  Answered 436 views 5 comments 0 points Most recent by asaki November 2017Ask the GATK team
• GATK depth of coverage

  Answered 896 views 1 comment 0 points Most recent by SkyWarrior October 2017Ask the GATK team
• HC listing depth one read less

  Answered 169 views 18 comments 0 points Most recent by Sheila October 2017Ask the GATK team
• DP differences between haploid and diploid mode

  Answered 298 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 127 views 1 comment 0 points Most recent by EADG September 2017Ask the GATK team
• DepthOfCoverage in v4

  Answered 77 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 93 views 2 comments 0 points Most recent by mankyua August 2017Ask the GATK team
• CalculateTargetCoverage error

  Answered 313 views 3 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• How to return an Array given as input

  Accepted Answer 194 views 2 comments 0 points Most recent by dbecker July 2017Ask the Cromwell + WDL Team
• What does the output of DepthOfCoverage means?

  Answered 3.1K 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 497 views 2 comments 0 points 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 98 views 2 comments 0 points Most recent by Nanda April 2017Ask the GATK team
• Allele frequency and depth VCF produced by MuTect2

  Answered 582 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2017Ask the GATK team
• Extremely high depth of coverage

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

  Answered 123 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 129 views 1 comment 0 points Most recent by Sheila October 2016Ask the GATK team
• Bug report: DepthOfCoverage csv output

  Answered 121 views 1 comment 0 points Most recent by Sheila September 2016Ask the GATK team
• DepthOfCoverage multiple samples

  Accepted Answer 383 views 4 comments 0 points Most recent by adri_somavilla August 2016Ask the GATK team
• Error in DepthOfCoverage for interval of 1bp

  Accepted Answer 161 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 2016Ask the GATK team
• DepthOfCoverage Genelist Error

  Answered 135 views 1 comment 0 points Most recent by Geraldine_VdAuwera June 2016Ask the GATK team
• interpreting depth of coverage

  Accepted Answer 321 views 1 comment 0 points Most recent by Sheila May 2016Ask the GATK team
• DepthOfCoverage -genelist: 'total coverage' and 'mean coverage' explanation

  Accepted Answer 407 views 0 comments 0 points Started by user31888 April 2016 Ask the GATK team
• GATK depthofcoverage runtimeerror: nullpointerexception

  Accepted Answer 384 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 551 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2016Ask the GATK team
• DepthOfCoverage run time 4.6 days?

  Answered 241 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 288 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 285 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 1.5K 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 248 views 1 comment 0 points Most recent by Geraldine_VdAuwera December 2015Ask the GATK team
• RE: Gene list headers

  Accepted Answer 951 views 3 comments 0 points Most recent by marlaux November 2015Ask the GATK team
• DepthOfCoverage memory usage

  Accepted Answer 489 views 6 comments 0 points Most recent by igor November 2015Ask the GATK team
• DepthOfCoverage missing to report some locations

  Answered 148 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 297 views 5 comments 0 points Most recent by wariobrega August 2015Ask the GATK team
• How to calulate base counts percentage?

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

  Answered 1.6K views 8 comments 0 points Most recent by Sheila July 2015Ask the GATK team
• disable NotPrimaryAlignmentFilter in DepthOfCoverage

  Answered 280 views 3 comments 0 points Most recent by Sheila July 2015Ask the GATK team
• Odd distribution of Coverage for GATK HaplotypeCaller Variants

  Answered 1.4K views 21 comments 0 points Most recent by Geraldine_VdAuwera July 2015Ask the GATK team
• DepthOfCoverage and DiagnoseTargets: our plans for development and support

  2.2K views 9 comments 0 points Most recent by Geraldine_VdAuwera June 2015Announcements
• DepthOfCoverage, QualifyMissingIntervals and DiagnoseTargets?

  Answered 404 views 4 comments 0 points Most recent by Blue May 2015Ask the GATK team
• variant detection: DP and Mendelization

  Accepted Answer 223 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 177 views 1 comment 0 points Most recent by Geraldine_VdAuwera March 2015Ask the GATK team
• which file to use as input to DepthOfCoverage?

  Answered 302 views 5 comments 0 points Most recent by Geraldine_VdAuwera March 2015Ask the GATK team
• % Depth at X vs cumulative_coverage_proportions

  Answered 222 views 1 comment 0 points Most recent by Sheila December 2014Ask the GATK team
• DepthOfCoverage summary reports too many bases

  Answered 1.9K 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 2.4K views 2 comments 0 points Most recent by gwilymh December 2014Ask the GATK team
• DepthOfCoverage interval_summary and interval_statistics

  Accepted Answer 741 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 425 views 4 comments 0 points Most recent by Geraldine_VdAuwera December 2014Ask the GATK team
• DepthOfCoverage error

  Answered 157 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 1.7K views 3 comments 0 points Most recent by Sheila November 2014Ask the GATK team
• Getting insertion counts

  Accepted Answer 665 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 272 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 384 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 232 views 2 comments 0 points Most recent by cparobek October 2014Ask the GATK team
• DepthOfCoverage calculateCoverageOverGenes missing genes

  Answered 457 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 691 views 5 comments 0 points Most recent by estif74 July 2014Ask the GATK team
• Feature Request: Parallelize more GATK tools

  Accepted Answer 281 views 2 comments 0 points Most recent by bredeson June 2014Ask the GATK team
• Minimum depth requirement when creating gVCFs files?

  Accepted Answer 721 views 8 comments 0 points Most recent by Geraldine_VdAuwera May 2014Ask the GATK team
• Depth of Coverage - Only one type of output

  Answered 2K views 8 comments 0 points Most recent by Geraldine_VdAuwera April 2014Ask the GATK team
• memory used by DepthOfCoverage

  Accepted Answer 1.2K views 3 comments 0 points Most recent by chunxuan March 2014Ask the GATK team
• BaseCoverageDistribution

  Accepted Answer 787 views 8 comments 0 points Most recent by avidLearner January 2014Ask the GATK team
• Is the parallelism documentation for DepthOfCoverage correct?

  Answered 624 views 8 comments 0 points Most recent by Shrey_S January 2014Ask the GATK team
• how does the tools DepthOfCoverage work?

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

  Accepted Answer 306 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2013Ask the GATK team
• DepthofCoverage

  Answered 492 views 3 comments 0 points Most recent by pdexheimer November 2013Ask the GATK team
• DepthOfCoverage for whole genome: skipped few regions

  Accepted Answer 527 views 5 comments 0 points Most recent by Geraldine_VdAuwera October 2013Ask the GATK team
• DepthOfCoverage

  Accepted Answer 610 views 7 comments 0 points Most recent by Geraldine_VdAuwera October 2013Ask the GATK team
• DepthOfCoverage (without -L option) output

  Accepted Answer 935 views 5 comments 0 points Most recent by Geraldine_VdAuwera October 2013Ask the GATK team
• DepthOfCoverage gene list Ensembl format

  Answered 870 views 1 comment 0 points Most recent by Geraldine_VdAuwera September 2013Ask the GATK team
• DepthOfCoverage multi-threading

  Accepted Answer 959 views 2 comments 0 points Most recent by tommycarstensen September 2013Ask the GATK team
• DP and chromosome filtering

  Accepted Answer 358 views 3 comments 0 points Most recent by Geraldine_VdAuwera July 2013Ask the GATK team
• DepthofCoverage Walker

  Accepted Answer 512 views 5 comments 0 points Most recent by pmudvari June 2013Ask the GATK team
• Undocumented change in 2.4? (-A DepthOfCoverage)

  Accepted Answer 900 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 452 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 294 views 2 comments 0 points Most recent by ge2sasag April 2013Ask the GATK team
• Concerns regarding transition from DepthOfCoverage to DiagnoseTargets.

  Accepted Answer 369 views 1 comment 0 points Most recent by Geraldine_VdAuwera March 2013Ask the GATK team
• Remove duplicate reads from the DepthOfCoverage

  Answered 1.7K views 3 comments 0 points Most recent by Geraldine_VdAuwera January 2013Ask the GATK team
• DepthOfCoverage Error

  Answered 1K views 2 comments 0 points Most recent by bgusr October 2012Ask the GATK team