Documentation Questions

Known Sites for BQSR Answered
- T. Li
- December 07, 2020 22:26
5 votes 5 comments
Where is the list of annotations and annotation groups? Answered
- tedtoal
- July 05, 2021 23:05
2 votes 7 comments
How does Mutect2 count read depth/coverage? Answered
- Sameer Shankar
- February 16, 2023 20:40
1 vote 11 comments
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
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
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
CallCopyRatioSegments -- how does it work? Answered
- Austin Southard-Smith
- February 10, 2023 20:46
0 votes 3 comments
Picard SortSam error Answered
- Tanay Biswas
- October 14, 2022 11:18
0 votes 3 comments
Issues with LiftoverVcf Answered
- Mohammad Deen Hayatu
- October 06, 2022 06:43
0 votes 6 comments
Too many duplicate articles Answered
- Дмитрий Голик
- September 09, 2022 09:14
0 votes 2 comments
ASEReadCount Only Outputting the First Chromosome Answered
- Leslie Youtsey
- August 31, 2022 19:31
0 votes 3 comments
ASEReadCounter outputting blank table Answered
- Leslie Youtsey
- August 24, 2022 17:53
- Edited
0 votes 4 comments
SamToFastq - bam order Answered
- Jakub Savara
- July 24, 2022 10:48
0 votes 6 comments
HaplotypeCaller using one sample split in two bam files Answered
- elena vigorito
- June 28, 2022 09:16
0 votes 3 comments
GATK genomicsDBImport error Answered
- @OK
- June 14, 2022 11:11
0 votes 3 comments
germline mutation calling using per-sample module Answered
- chenglei
- June 08, 2022 16:06
0 votes 2 comments
Haplotypecaller Answered
- Mahdi Ahmadi
- May 30, 2022 16:45
0 votes 1 comment
BaseRecalibrator --max-cycle Answered
- oğuzhan karaosmanoğlu
- May 12, 2022 11:11
0 votes 1 comment
Question on Java version Answered
- Anand
- May 10, 2022 15:24
0 votes 2 comments
GATK CNV somatic panels of normal design Answered
- Mallika Gandham
- May 04, 2022 16:07
0 votes 3 comments
JointGermlineCNVSegmentation Answered
- Yangyxt
- April 30, 2022 06:56
0 votes 2 comments
GetPileupSummaries common germline variant sites VCF hg38 Answered
- Anish K
- April 18, 2022 16:48
0 votes 2 comments
how to run "gatk-register"? Answered
- Mahendra Singh
- March 28, 2022 04:28
0 votes 2 comments
MergeBamAlignment for mitochondrial variant discovery Answered
- Ahmed S. Chakroun
- March 18, 2022 17:33
0 votes 1 comment
Is FilterAlignmentArtifacts out of the Mutect2 calling best practices? Answered
- shenglai
- March 11, 2022 01:53
0 votes 1 comment

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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.