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Ask the GATK team
Archives for July 2014
Discussion List
Handling Multimappers
Accepted Answer
613
views
4
comments
0
points
Most recent by
bruce01
July 2014
Ask the GATK team
Supported SNPeff version with GATK
Answered
517
views
9
comments
0
points
Most recent by
Gesseca
January 2015
Ask the GATK team
New To GATK , WGS Germline/Tumor Data ~ OK for GATK ?
Answered
104
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
VariantRecalibrator raising the number of variants used to train the negative model question
Accepted Answer
322
views
5
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
pre-processing reads and non-model BQSR
Accepted Answer
745
views
4
comments
0
points
Most recent by
ritamichelle
July 2014
Ask the GATK team
Argument with name 'knownSites' isn't defined
1.4K
views
5
comments
0
points
Most recent by
palmeira
September 2014
Ask the GATK team
bam to fasta
Answered
1.2K
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
StrandBiasbySample, FisherStrand Annotation
Accepted Answer
1.1K
views
14
comments
1
point
Most recent by
Sheila
September 2016
Ask the GATK team
What's the base of VQSLOD
Accepted Answer
294
views
2
comments
0
points
Most recent by
tennis_music
July 2014
Ask the GATK team
"FilteredInAll" VariantEval category
Question
548
views
8
comments
0
points
Most recent by
eflynn90
July 2014
Ask the GATK team
Help need to fix the error while running DepthofCoverage
Answered
132
views
1
comment
0
points
Most recent by
pdexheimer
July 2014
Ask the GATK team
What factors influence the runtime of filtering vcf files?
Accepted Answer
134
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
confusion about this documents: How should I interpret VCF files produced by the GATK?
Answered
542
views
11
comments
0
points
Most recent by
dainguyen
December 2014
Ask the GATK team
CPU usage
Answered
378
views
5
comments
0
points
Most recent by
TechnicalVault
November 2014
Ask the GATK team
ContESt for WGS data
Answered
467
views
15
comments
0
points
Most recent by
Sheila
September 2016
Ask the GATK team
Parallelization at core level for RealignerTargetCreator and IndelRealigner?
Accepted Answer
357
views
5
comments
0
points
Most recent by
Sheila
July 2014
Ask the GATK team
possible issue with VCF files made by GenotypeGVCFs in 3.2-2??
Answered
406
views
4
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Maven build error in current git
Accepted Answer
1.1K
views
7
comments
0
points
Most recent by
Geraldine_VdAuwera
August 2014
Ask the GATK team
How Can I Get strand Bias Imformation From Mutect?
Accepted Answer
1K
views
5
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Problem running RealignerTargetCreator
Accepted Answer
482
views
2
comments
0
points
Most recent by
gedoardo83
July 2014
Ask the GATK team
DiagnoseTargets: NO_READS and COVERAGE filters
Accepted Answer
317
views
6
comments
0
points
Most recent by
Sheila
August 2014
Ask the GATK team
HaplotypeCaller call SNP and indel .
419
views
12
comments
0
points
Most recent by
xiaoyun
July 2014
Ask the GATK team
Variant Calling of a personal genome : USAGE question
Accepted Answer
243
views
4
comments
0
points
Most recent by
Nilaksha
July 2014
Ask the GATK team
Haplotype Caller - incorrect DP with medium coverage data and missed tri-allelic sites
Accepted Answer
592
views
6
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
depth of coverage link
Accepted Answer
619
views
5
comments
0
points
Most recent by
estif74
July 2014
Ask the GATK team
Expected runtime for GenotypeGVCFs -- taking long time
Accepted Answer
749
views
6
comments
0
points
Most recent by
pdexheimer
July 2014
Ask the GATK team
realignment of bam files
Answered
169
views
7
comments
0
points
Most recent by
ratanchopra
July 2014
Ask the GATK team
QUAL vs. Ts/Tv correlations , for hgh QUAL values
Accepted Answer
795
views
8
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
BaseRecalibrator : problem in vcf files
Answered
469
views
1
comment
0
points
Most recent by
thibault
July 2014
Ask the GATK team
Resource bundle location
Answered
359
views
5
comments
0
points
Most recent by
deepak_grover
July 2014
Ask the GATK team
Resource bundle location
Answered
107
views
2
comments
0
points
Most recent by
Geraldine_VdAuwera
September 2014
Ask the GATK team
Variant Recalibration failing
Answered
1.3K
views
27
comments
0
points
Most recent by
shlee
May 2017
Ask the GATK team
Issues with Base Quality Score Recalibration
Answered
621
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
dbSNP138 vs dbSNP141 version in GATK Bundle
Accepted Answer
1.2K
views
5
comments
0
points
Most recent by
Sheila
August 2014
Ask the GATK team
Can -nct/-nt option in UnifiedGenotyper make different vcfs?
Answered
600
views
1
comment
0
points
Most recent by
Sheila
July 2014
Ask the GATK team
Unified genotyper
Answered
136
views
1
comment
0
points
Most recent by
Sheila
July 2014
Ask the GATK team
0/0 genotypes with no associated AD
Accepted Answer
232
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
select variants documentation
Accepted Answer
322
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
which input files for IndelRealigner and BaseRecalibrator?
Accepted Answer
1.3K
views
2
comments
0
points
Most recent by
KinMok
July 2014
Ask the GATK team
GenotypeGVCF -allSites --includeNonVariantSites option
Accepted Answer
542
views
2
comments
0
points
Most recent by
prepagam
July 2014
Ask the GATK team
The reference fasta for hg19 from your resource bundle is not readable by PicardTools reorder
Answered
1.2K
views
4
comments
0
points
Most recent by
Geraldine_VdAuwera
November 2014
Ask the GATK team
HaplotypeCaller active regions
Accepted Answer
1.1K
views
5
comments
0
points
Most recent by
Geraldine_VdAuwera
October 2015
Ask the GATK team
GenotypeGVCFs remaining runtime estimate incorrect
Question
519
views
4
comments
0
points
Most recent by
tommycarstensen
July 2014
Ask the GATK team
GT:AD:DP:GQ:PL instead of GT:DP:GQ when merging two vcf files with more than two alleles
Answered
1K
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
I have a error message that Index 25, size 8.
Answered
315
views
6
comments
0
points
Most recent by
weiqiang
July 2014
Ask the GATK team
CatVariants not working?
Accepted Answer
1.5K
views
7
comments
0
points
Most recent by
gipelttil
July 2014
Ask the GATK team
combineGVCF bug?
Answered
668
views
19
comments
0
points
Most recent by
jhomsy
August 2014
Ask the GATK team
IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2)
Accepted Answer
823
views
7
comments
0
points
Most recent by
Geraldine_VdAuwera
November 2014
Ask the GATK team
low quality variants
Accepted Answer
189
views
2
comments
0
points
Most recent by
Jayce
July 2014
Ask the GATK team
problem with queue job reports in 3.2-0
Answered
495
views
3
comments
0
points
Most recent by
jam
July 2014
Ask the GATK team
NHLBI Exome Sequencing Project ESP indel
Answered
506
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Loss of Reads in HCMappingQualityFilter
Answered
1.1K
views
21
comments
0
points
Most recent by
Geraldine_VdAuwera
December 2016
Ask the GATK team
Problem building gatk-protected from github
Accepted Answer
1.3K
views
7
comments
0
points
Most recent by
Johan_Dahlberg
July 2014
Ask the GATK team
Recall variants with haplotypeCaller
Accepted Answer
185
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
AD field doesn't update after merging GVCF files with GenotypeGVCFs
Accepted Answer
301
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Oncotator Splice Isoform Annotations
Accepted Answer
278
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Splice Isoform Annotations in Oncotator
Question
98
views
0
comments
0
points
Started by
emcmillan
July 2014
Ask the GATK team
Realigner Target Creator does not realign correctly with known indel
Answered
725
views
7
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Indelrealignment
Answered
465
views
7
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
GVCF error - Argument emitRefConfidence has a bad value
Accepted Answer
606
views
4
comments
0
points
Most recent by
vifehe
April 2015
Ask the GATK team
HAPLOTYPER ROI PARALELITATION
78
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
How do you calculate MQ?
Accepted Answer
913
views
7
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Known sites for Base Recalibration and Variant Quality Score Recalibration
Answered
875
views
21
comments
0
points
Most recent by
Geraldine_VdAuwera
January 2015
Ask the GATK team
Cannot downsample using printReads an -dcov parameter. No effect over original bam observed.
Answered
863
views
10
comments
0
points
Most recent by
TechnicalVault
December 2014
Ask the GATK team
Varinat calling from Multisample RNAseq data???
Answered
359
views
2
comments
0
points
Most recent by
tejas
July 2014
Ask the GATK team
ClippingRankSumTest - Hard clipped bases only
Accepted Answer
113
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
RegenotypeVariants
Accepted Answer
232
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Understanding the Output from GenotypeGVCFs
Answered
202
views
2
comments
0
points
Most recent by
JonathonBlake
July 2014
Ask the GATK team
VariantEval and FunctionalClass: missing SNP class data from tables - any help for newbie.
Accepted Answer
206
views
2
comments
0
points
Most recent by
drmtbishop
July 2014
Ask the GATK team
Zero INDELs from UnifiedGenotyper from 74 samples
Accepted Answer
167
views
2
comments
0
points
Most recent by
tinu
July 2014
Ask the GATK team
Anyone attending the ISMB 2014 conference July 13 - 15 here?
Answered
169
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
How to get the number of forward/reverse reads in the final VCF output?
Answered
397
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Variant discovery in aneuploid organisms
Accepted Answer
385
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Sensible ways to split CombineGVCFs
Accepted Answer
825
views
13
comments
1
point
Most recent by
Geraldine_VdAuwera
July 2017
Ask the GATK team
How to make RealignerTargetCreator more sensitive
Accepted Answer
249
views
7
comments
0
points
Most recent by
fborja
July 2014
Ask the GATK team
VQSR filter
Answered
187
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
HaplotypeCaller and GPU
Accepted Answer
437
views
2
comments
0
points
Most recent by
kwyattm
July 2014
Ask the GATK team
long indel by GATK unified genotyper
Answered
185
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
GATK-BaseRecalibrator run error
107
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
Unified Genotyper: Maximum sensitivity
Accepted Answer
314
views
5
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
IndelRealigner -nWayOut: Possible to specify output directory?
Accepted Answer
990
views
7
comments
0
points
Most recent by
Sheila
October 2014
Ask the GATK team
GATK Variant caller- unifiedGenotyper input BAM file
196
views
4
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
SplitNCigarReads complains about N in CIGAR
Answered
2K
views
16
comments
0
points
Most recent by
Geraldine_VdAuwera
September 2016
Ask the GATK team
ERROR MESSAGE: For input string: "." when validating variants
8.8K
views
2
comments
0
points
Most recent by
baesc
July 2014
Ask the GATK team
VQSR VariantRecalibrator Rplot
Accepted Answer
517
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team
BQSR: empirical vs. recorded base quality
Answered
453
views
4
comments
0
points
Most recent by
mayaab
July 2014
Ask the GATK team
VariantFiltration and VariantRecalibrator
Answered
372
views
5
comments
0
points
Most recent by
Sheila
July 2014
Ask the GATK team
How to estimate heap size (-Xmx) necessary to call variants using Unified Genotyper?
Accepted Answer
1.2K
views
11
comments
0
points
Most recent by
Geraldine_VdAuwera
May 2015
Ask the GATK team
How do I get Indelocator?
Accepted Answer
382
views
7
comments
0
points
Most recent by
egeulgen
August 2015
Ask the GATK team
BAM malformed verification tool?
Accepted Answer
203
views
1
comment
0
points
Most recent by
Sheila
July 2014
Ask the GATK team
run CombineGVCFs per chromosome and merge with CatVariants?
Accepted Answer
1.1K
views
8
comments
0
points
Most recent by
Lavanya
May 2015
Ask the GATK team
GENOTYPE_GIVEN_ALLELES mode in HaplotypeCaller
Answered
757
views
3
comments
0
points
Most recent by
Sheila
October 2014
Ask the GATK team
Input files reads and reference have incompatible contigs
Answered
782
views
10
comments
0
points
Most recent by
wukhan
September 2015
Ask the GATK team
About the binned quality scores of Illumina Hiseq X 10
Accepted Answer
707
views
2
comments
0
points
Most recent by
luciaUY
July 2014
Ask the GATK team
Combine gVFC and GenotypeGVCFs
Accepted Answer
456
views
6
comments
0
points
Most recent by
tberner
July 2014
Ask the GATK team
merging bam files for an individual
Accepted Answer
1.1K
views
3
comments
0
points
Most recent by
eflynn90
July 2014
Ask the GATK team
Oncotator run error: Could not find config file (maflite_input.config)
Accepted Answer
451
views
2
comments
0
points
Most recent by
pratikchandrani
July 2014
Ask the GATK team
can I strip out BD/BI stings after creating gvcf in the new 3.1 workflow?
Accepted Answer
270
views
6
comments
0
points
Most recent by
Geraldine_VdAuwera
July 2014
Ask the GATK team