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depthofcoverage
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Discussion List
GATK4 does not include DepthOfCoverage tool
957
views
12
comments
0
points
Most recent by
FPBarthel
February 12
Ask the GATK team
Analysis Pipeline Discrepancy in SNP Calling and Coverage
Answered
30
views
3
comments
0
points
Most recent by
AdelaideR
February 5
Ask 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 2018
Ask the GATK team
Same pipeline for exome seq variant calling with different results
35
views
1
comment
0
points
Most recent by
bhanuGandham
November 2018
Ask the GATK team
Using depth of coverage metrics for variant evaluation
2.6K
views
13
comments
1
point
Most recent by
tytolin
October 2018
Methods 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 2018
Ask the GATK team
How to generate RefSeq ROD
Accepted Answer
2.2K
views
10
comments
0
points
Most recent by
shlee
August 2018
Ask the GATK team
How to calculate minReadsAtLocus
Answered
20
views
1
comment
0
points
Most recent by
Sheila
July 2018
Ask the GATK team
Depth with and without Soft-Clipping
Answered
88
views
3
comments
0
points
Most recent by
Sheila
May 2018
Ask the GATK team
DepthOfCoverage
Accepted Answer
185
views
1
comment
0
points
Most recent by
Sheila
May 2018
Ask 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 2018
Ask 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 2018
Ask the GATK team
DepthOfCoverage fails with java.lang.ArithmeticException: / by zero
Answered
51
views
1
comment
0
points
Most recent by
Sheila
March 2018
Ask the GATK team
Depth of coverage in GATK 4
1K
views
2
comments
0
points
Most recent by
scottfrod
March 2018
Ask 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 2017
Ask the GATK team
Abnormally high per-sample depth after running GenotypeGVCFs
Answered
42
views
1
comment
0
points
Most recent by
Sheila
November 2017
Ask the GATK team
Different coverage metrics between GATK and PICARD
Answered
436
views
5
comments
0
points
Most recent by
asaki
November 2017
Ask the GATK team
GATK depth of coverage
Answered
896
views
1
comment
0
points
Most recent by
SkyWarrior
October 2017
Ask the GATK team
HC listing depth one read less
Answered
169
views
18
comments
0
points
Most recent by
Sheila
October 2017
Ask the GATK team
DP differences between haploid and diploid mode
Answered
298
views
9
comments
0
points
Most recent by
Sheila
October 2017
Ask 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 2017
Ask the GATK team
DepthOfCoverage in v4
Answered
77
views
1
comment
0
points
Most recent by
Sheila
August 2017
Ask 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 2017
Ask the GATK team
CalculateTargetCoverage error
Answered
313
views
3
comments
0
points
Most recent by
Sheila
August 2017
Ask the GATK team
How to return an Array given as input
Accepted Answer
194
views
2
comments
0
points
Most recent by
dbecker
July 2017
Ask the Cromwell + WDL Team
What does the output of DepthOfCoverage means?
Answered
3.1K
views
5
comments
0
points
Most recent by
Sheila
May 2017
Ask the GATK team
depth of coverage from gVCF files
Accepted Answer
1.1K
views
5
comments
0
points
Most recent by
Sheila
May 2017
Ask the GATK team
GATK DepthOfCoverage
Accepted Answer
497
views
2
comments
0
points
Most recent by
vesna_pajic
April 2017
Ask 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 2017
Ask the GATK team
Allele frequency and depth VCF produced by MuTect2
Answered
582
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
February 2017
Ask the GATK team
Extremely high depth of coverage
375
views
4
comments
0
points
Most recent by
adri_somavilla
February 2017
Ask the GATK team
DepthOfCoverage takes many hours to run
Answered
123
views
3
comments
0
points
Most recent by
Sheila
February 2017
Ask the GATK team
Downsampling Experiment
Accepted Answer
1.1K
views
8
comments
0
points
Most recent by
Geraldine_VdAuwera
December 2016
Ask 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 2016
Ask the GATK team
Bug report: DepthOfCoverage csv output
Answered
121
views
1
comment
0
points
Most recent by
Sheila
September 2016
Ask the GATK team
DepthOfCoverage multiple samples
Accepted Answer
383
views
4
comments
0
points
Most recent by
adri_somavilla
August 2016
Ask the GATK team
Error in DepthOfCoverage for interval of 1bp
Accepted Answer
161
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2016
Ask the GATK team
DepthOfCoverage Genelist Error
Answered
135
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
June 2016
Ask the GATK team
interpreting depth of coverage
Accepted Answer
321
views
1
comment
0
points
Most recent by
Sheila
May 2016
Ask 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 2016
Ask 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 2016
Ask the GATK team
DepthOfCoverage run time 4.6 days?
Answered
241
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
February 2016
Ask the GATK team
Discrepancy between GATK DepthOfCoverage and samtools mpileup - depth values
Answered
288
views
1
comment
0
points
Most recent by
Sheila
February 2016
Ask 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 2016
Ask 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 2016
Ask 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 2015
Ask the GATK team
RE: Gene list headers
Accepted Answer
951
views
3
comments
0
points
Most recent by
marlaux
November 2015
Ask the GATK team
DepthOfCoverage memory usage
Accepted Answer
489
views
6
comments
0
points
Most recent by
igor
November 2015
Ask the GATK team
DepthOfCoverage missing to report some locations
Answered
148
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
October 2015
Ask 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 2015
Ask the GATK team
How to calulate base counts percentage?
210
views
1
comment
0
points
Most recent by
Sheila
July 2015
Ask 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 2015
Ask the GATK team
disable NotPrimaryAlignmentFilter in DepthOfCoverage
Answered
280
views
3
comments
0
points
Most recent by
Sheila
July 2015
Ask 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 2015
Ask 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 2015
Announcements
DepthOfCoverage, QualifyMissingIntervals and DiagnoseTargets?
Answered
404
views
4
comments
0
points
Most recent by
Blue
May 2015
Ask the GATK team
variant detection: DP and Mendelization
Accepted Answer
223
views
1
comment
0
points
Most recent by
Sheila
May 2015
Ask the GATK team
Coverage per gene by Exons intervals hg19
Accepted Answer
1.1K
views
2
comments
0
points
Most recent by
mariagr
April 2015
Ask the GATK team
How does DepthofCoverage treat half-mapped reads?
Accepted Answer
177
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
March 2015
Ask the GATK team
which file to use as input to DepthOfCoverage?
Answered
302
views
5
comments
0
points
Most recent by
Geraldine_VdAuwera
March 2015
Ask the GATK team
% Depth at X vs cumulative_coverage_proportions
Answered
222
views
1
comment
0
points
Most recent by
Sheila
December 2014
Ask the GATK team
DepthOfCoverage summary reports too many bases
Answered
1.9K
views
41
comments
0
points
Most recent by
JamesM
December 2014
Ask 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 2014
Ask the GATK team
DepthOfCoverage interval_summary and interval_statistics
Accepted Answer
741
views
4
comments
0
points
Most recent by
Geraldine_VdAuwera
December 2014
Ask 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 2014
Ask the GATK team
DepthOfCoverage error
Answered
157
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
November 2014
Ask 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 2014
Ask the GATK team
Getting insertion counts
Accepted Answer
665
views
8
comments
0
points
Most recent by
Geraldine_VdAuwera
November 2014
Ask 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 2014
Ask the GATK team
Exon output Depth of Coverage
Accepted Answer
1.9K
views
4
comments
0
points
Most recent by
mehar
November 2014
Ask the GATK team
DepthofCoverage, argument with name 'includeRefNSites' isn't defined?
Accepted Answer
384
views
6
comments
0
points
Most recent by
stevenlovesscience
November 2014
Ask 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 2014
Ask the GATK team
DepthOfCoverage calculateCoverageOverGenes missing genes
Answered
457
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
October 2014
Ask 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 2014
Ask the GATK team
depth of coverage link
Accepted Answer
691
views
5
comments
0
points
Most recent by
estif74
July 2014
Ask the GATK team
Feature Request: Parallelize more GATK tools
Accepted Answer
281
views
2
comments
0
points
Most recent by
bredeson
June 2014
Ask the GATK team
Minimum depth requirement when creating gVCFs files?
Accepted Answer
721
views
8
comments
0
points
Most recent by
Geraldine_VdAuwera
May 2014
Ask the GATK team
Depth of Coverage - Only one type of output
Answered
2K
views
8
comments
0
points
Most recent by
Geraldine_VdAuwera
April 2014
Ask the GATK team
memory used by DepthOfCoverage
Accepted Answer
1.2K
views
3
comments
0
points
Most recent by
chunxuan
March 2014
Ask the GATK team
BaseCoverageDistribution
Accepted Answer
787
views
8
comments
0
points
Most recent by
avidLearner
January 2014
Ask the GATK team
Is the parallelism documentation for DepthOfCoverage correct?
Answered
624
views
8
comments
0
points
Most recent by
Shrey_S
January 2014
Ask the GATK team
how does the tools DepthOfCoverage work?
374
views
4
comments
0
points
Most recent by
ahda
December 2013
Ask 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 2013
Ask the GATK team
DepthofCoverage
Answered
492
views
3
comments
0
points
Most recent by
pdexheimer
November 2013
Ask the GATK team
DepthOfCoverage for whole genome: skipped few regions
Accepted Answer
527
views
5
comments
0
points
Most recent by
Geraldine_VdAuwera
October 2013
Ask the GATK team
DepthOfCoverage
Accepted Answer
610
views
7
comments
0
points
Most recent by
Geraldine_VdAuwera
October 2013
Ask the GATK team
DepthOfCoverage (without -L option) output
Accepted Answer
935
views
5
comments
0
points
Most recent by
Geraldine_VdAuwera
October 2013
Ask the GATK team
DepthOfCoverage gene list Ensembl format
Answered
870
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
September 2013
Ask the GATK team
DepthOfCoverage multi-threading
Accepted Answer
959
views
2
comments
0
points
Most recent by
tommycarstensen
September 2013
Ask the GATK team
DP and chromosome filtering
Accepted Answer
358
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2013
Ask the GATK team
DepthofCoverage Walker
Accepted Answer
512
views
5
comments
0
points
Most recent by
pmudvari
June 2013
Ask the GATK team
Undocumented change in 2.4? (-A DepthOfCoverage)
Accepted Answer
900
views
11
comments
1
point
Most recent by
Carneiro
May 2013
Ask the GATK team
bam is malformed depthofcoverage
Answered
1.6K
views
3
comments
0
points
Most recent by
remimaglione
May 2013
Ask the GATK team
DepthOfCoverage producing "extremely high quality score" error
Accepted Answer
1.9K
views
12
comments
0
points
Most recent by
Carneiro
May 2013
Ask the GATK team
Depth of Coverage - reported only first exon
Answered
452
views
4
comments
0
points
Most recent by
MarcelaD
May 2013
Ask 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 2013
Ask the GATK team
Concerns regarding transition from DepthOfCoverage to DiagnoseTargets.
Accepted Answer
369
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
March 2013
Ask the GATK team
Remove duplicate reads from the DepthOfCoverage
Answered
1.7K
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
January 2013
Ask the GATK team
DepthOfCoverage Error
Answered
1K
views
2
comments
0
points
Most recent by
bgusr
October 2012
Ask the GATK team
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