Documentation Questions

is --dont-use-soft-clipped-bases discarded in HaplotypeCaller?
- Songming Liu
- March 24, 2023 07:45
0 votes 0 comments
Genotype filtering still write "PASS" in filter field
- Marissa Eronika
- March 21, 2023 15:50
1 vote 1 comment
Why is the coverage cut abruptly for a region in the bamout file of Mutect2 in comparison to the region in input files?
- ISmolicz
- March 21, 2023 00:15
0 votes 1 comment
Using haplotype information from high-coverage samples as a prior for Haplotypecaller for other low-coverage samples in the same dataset?
- Nils Paffen
- March 07, 2023 16:43
0 votes 1 comment
Picard CollectHsMetrics PCT_TARGET_BASES Output
- michaelmc
- February 23, 2023 17:04
0 votes 2 comments
error:Argument --emit-ref-confidence
- Rezwan Tariq
- February 22, 2023 10:09
0 votes 0 comments
Funcotator 4.1.2.0 gencode for locatableXSV
- Frank Maiwald
- February 20, 2023 11:55
0 votes 1 comment
Intervals and GenomicsDBImport
- Irbin Manuel Veliz Isidro
- February 17, 2023 09:35
0 votes 2 comments
How does Mutect2 count read depth/coverage? Answered
- Sameer Shankar
- February 16, 2023 20:40
1 vote 11 comments
CallCopyRatioSegments -- how does it work? Answered
- Austin Southard-Smith
- February 10, 2023 20:46
0 votes 3 comments
gatk SelectVariant identified no snps in the vsf file while it has 63702926 snps
- Vishal Negi
- February 06, 2023 19:24
0 votes 1 comment
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
Report file CreateExtendedIlluminaManifest Report file
- James Gallant
- October 31, 2022 15:28
1 vote 1 comment
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
CalculateFingerprintMetrics Usability On Somatic Samples
- Kathryn Kananen
- September 13, 2022 04:16
- Edited
0 votes 1 comment
Request: examples of svtk usage
- Yaping Wu
- September 10, 2022 01:30
0 votes 1 comment
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

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.