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Rounds of BQSR in GATK3 GenericPreProcessingWorkflow
Accepted Answer
22
views
4
comments
0
points
Most recent by
AdelaideR
January 29
Ask the GATK team
Generating a vcf with the information of specific genome positions (hotspots)
Answered
39
views
3
comments
0
points
Most recent by
SChaluvadi
December 2018
Ask the GATK team
Add GATK3 Variant Refinement
Accepted Answer
34
views
5
comments
0
points
Most recent by
SChaluvadi
November 2018
Ask the FireCloud Team
GATK4 vs GATK3 output file compatability
Accepted Answer
63
views
2
comments
0
points
Most recent by
map2085
July 2018
Ask the GATK team
i am running haplotypcaller in one bam file
Answered
70
views
1
comment
0
points
Most recent by
Sheila
June 2018
Ask the GATK team
GATK4 Realign around indels
Answered
145
views
1
comment
0
points
Most recent by
Sheila
February 2018
Ask the GATK team
CombineVariants Key . found in VariantContext field INFO but this key isn't defined in the VCFHeader
Answered
239
views
3
comments
0
points
Most recent by
Sheila
February 2018
Ask the GATK team
Mutect2 outputting samples with AD of "."
Answered
30
views
3
comments
0
points
Most recent by
Sheila
February 2018
Ask the GATK team
Testing Intel Arria® 10 GX FPGA implementation of HaplotypeCaller (PairHMM)
Answered
255
views
3
comments
0
points
Most recent by
agosto
February 2018
Ask the GATK team
Release notes for GATK version 3.8
369
views
0
comments
0
points
Started by
Geraldine_VdAuwera
July 2017
Announcements
Anticipate "--fix_misencoded_quality_scores"
Accepted Answer
165
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
April 2017
Ask the GATK team
gatk haplotypecaller for gvcf
Answered
142
views
2
comments
0
points
Most recent by
Geraldine_VdAuwera
December 2016
Ask the GATK team
Release notes for GATK version 3.7
598
views
0
comments
0
points
Started by
Geraldine_VdAuwera
December 2016
Announcements
Release notes for GATK version 3.6
1.8K
views
3
comments
0
points
Most recent by
Geraldine_VdAuwera
June 2016
Announcements
Release notes for GATK version 3.5
1.5K
views
7
comments
0
points
Most recent by
Geraldine_VdAuwera
February 2016
Announcements
Release notes for GATK version 3.4
2.3K
views
27
comments
0
points
Most recent by
Sheila
September 2015
Announcements
Release notes for GATK version 3.3
1.7K
views
2
comments
0
points
Most recent by
Geraldine_VdAuwera
February 2015
Announcements
Workflow for fungal WGS
709
views
3
comments
0
points
Most recent by
simono101
January 2015
Ask the GATK team
GATK3 ApplyRecalibration doesn't work
Answered
395
views
2
comments
0
points
Most recent by
shazly
October 2014
Ask the GATK team
Introduction to the GATK Best Practices workflows
5.4K
views
3
comments
0
points
Most recent by
michaelchao
October 2014
Methods and Algorithms
GenotypeGVCFs
Answered
267
views
1
comment
0
points
Most recent by
Geraldine_VdAuwera
September 2014
Ask the GATK team
Minor license text updates for GATK 3.x
255
views
2
comments
0
points
Most recent by
Geraldine_VdAuwera
September 2014
Announcements
Question about CombineGVCFs results
Accepted Answer
365
views
6
comments
0
points
Most recent by
srynearson1
June 2014
Ask the GATK team
GATK 3.0+ LOD issue with VariantRecalibrator Running Large data sets .
Accepted Answer
341
views
4
comments
0
points
Most recent by
srynearson1
May 2014
Ask the GATK team
Slides from the 4/10 webinar on GATK 3 features
289
views
2
comments
0
points
Most recent by
Geraldine_VdAuwera
May 2014
Announcements
Special webinar on GATK 3 features (4/10)
239
views
0
comments
0
points
Started by
Geraldine_VdAuwera
April 2014
Announcements
GATK3.0 walker log output goes to stderr instead of stdout
Accepted Answer
290
views
1
comment
0
points
Most recent by
pdexheimer
March 2014
Ask the GATK team