Documentation Questions

Known Sites for BQSR Answered
- T. Li
- December 07, 2020 22:26
5 votes 5 comments
Difference between the different annotation groups available in GATK
- Shashank Nagaraja
- October 04, 2021 22:15
2 votes 1 comment
Where is the list of annotations and annotation groups? Answered
- tedtoal
- July 05, 2021 23:05
2 votes 7 comments
gCNV
- Sabrina Camp
- June 24, 2020 10:13
2 votes 1 comment
GATK4.1.5 GenotypeGVCFs --annotation-group
- hana lango allen
- March 12, 2020 16:06
2 votes 1 comment
Report file CreateExtendedIlluminaManifest Report file
- James Gallant
- October 31, 2022 15:28
1 vote 1 comment
Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller Answered
- Blaz Vrhovsek
- June 30, 2022 11:27
1 vote 1 comment
Documentation for running GATK and Cromwell on IBM Cloud Answered
- Takeshi Yoshimura
- April 05, 2022 01:24
1 vote 7 comments
genotyping calls don't align with coverage Answered
- Gertjan Wils
- March 15, 2022 12:57
1 vote 1 comment
Confirmation that Mutect2 /haplotype caller only use reads mapped within the active region
- JW
- June 03, 2021 16:19
1 vote 3 comments
Where do I find guidance on when to mark duplicates a second time? Answered
- ISmolicz
- November 13, 2020 11:54
1 vote 2 comments
Germline Resouce Answered
- happyhihello
- July 31, 2020 17:23
1 vote 3 comments
How to find or generate common germline variant sites VCF required by GetPileupSummaries
- Antti Koskenalho
- May 27, 2020 06:22
1 vote 4 comments
CollectAllelicCounts interval_list Answered
- jejacobs23
- May 18, 2020 22:33
1 vote 15 comments
vcf files for BQSR step Answered
- Varun Gupta
- March 30, 2020 22:13
1 vote 4 comments
GATK Best Practices Mitochondrial Analysis Answered
- ajwils
- January 09, 2020 21:15
- Edited
1 vote 45 comments
Variables harmonization tutorial for variables collected from Pic-sure from various cohort
- kei_hang_chan
- January 26, 2023 06:18
0 votes 0 comments
Picard's CollectRnaSeqMetrics
- Benli Chai
- January 17, 2023 20:36
0 votes 0 comments
Detailed reason for filtering by FilterMutectCalls
- tan qiang
- January 13, 2023 07:44
0 votes 0 comments
How to specify number of threads while running Mutect2
- Tanay Biswas
- December 21, 2022 05:49
0 votes 0 comments
Best practice trios
- Sheryl
- November 23, 2022 00:58
- Edited
0 votes 0 comments
BuildBamIndex
- Robert Bremel
- November 08, 2022 20:27
0 votes 4 comments
Java exception: index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
- Julián García-Abadillo
- October 27, 2022 13:37
- Edited
0 votes 2 comments
Can't access google cloud it says permission required
- HQ Zhao
- October 27, 2022 02:03
0 votes 2 comments
RGID versus RGPU
- Jean-Michel Carter
- October 20, 2022 06:49
- Edited
0 votes 1 comment
Picard SortSam error Answered
- Tanay Biswas
- October 14, 2022 11:18
0 votes 3 comments
Mutect2 produces 0 results for somatic mutation calling of paired-end reads (BAM)
- Di Pan
- October 09, 2022 05:22
- Edited
0 votes 1 comment
Issues with LiftoverVcf Answered
- Mohammad Deen Hayatu
- October 06, 2022 06:43
0 votes 6 comments
Documentation for interval files in resource bundle
- Laura Egolf
- September 19, 2022 21:28
0 votes 1 comment
UmiAwareMarkDuplicatesWithMateCigar - UMI_METRICS
- Miguel Grau
- September 13, 2022 10:55
- Edited
0 votes 2 comments

Welcome

GATK Team Out of Office

The GATK team will be out of office during December 9th 2022 to January 9th 2022 in observance of the holidays. We will not be able to answer posts from within this period. If you are still experiencing issues when we are back, please re-post your inquiry.