Documentation Questions

Known Sites for BQSR Answered
- T. Li
- December 07, 2020 22:26
5 votes 5 comments
How does Mutect2 count read depth/coverage? Answered
- Sameer Shankar
- February 16, 2023 20:40
2 votes 11 comments
Where is the list of annotations and annotation groups? Answered
- tedtoal
- July 05, 2021 23:05
2 votes 7 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 6 comments
how to run "gatk-register"? Answered
- Mahendra Singh
- March 28, 2022 04:28
0 votes 3 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

Genome Analysis Toolkit

Need Help?

Community Forum

Documentation Questions

Welcome

Didn't find what you were looking for?

Quick Links

Recent GATK News

About the GATK community