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 0 comments
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 0 comments
How does Mutect2 count read depth/coverage? Answered
- Sameer Shankar
- February 16, 2023 20:40
1 vote 11 comments
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
Intervals and GenomicsDBImport
- Irbin Manuel Veliz Isidro
- February 17, 2023 09:35
0 votes 2 comments
Picard CollectHsMetrics PCT_TARGET_BASES Output
- michaelmc
- February 23, 2023 17:04
0 votes 2 comments
Funcotator 4.1.2.0 gencode for locatableXSV
- Frank Maiwald
- February 20, 2023 11:55
0 votes 1 comment
error:Argument --emit-ref-confidence
- Rezwan Tariq
- February 22, 2023 10:09
0 votes 0 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
Why don't I have access to some links? Answered
- Manuel
- January 12, 2022 11:13
0 votes 3 comments
GATK Mutect2 tumor vs. normal sample Answered
- Enrico Cocchi
- October 02, 2020 16:23
0 votes 4 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
Should we run MarkDuplicates on PCR-Free Libraries made using PCR-Free Kits to take care of Optical Duplicates ?
- rohit satyam
- July 28, 2020 20:28
- Edited
0 votes 3 comments
BuildBamIndex
- Robert Bremel
- November 08, 2022 20:27
0 votes 4 comments
Best practice trios
- Sheryl
- November 23, 2022 00:58
- Edited
0 votes 0 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
vcf files for BQSR step Answered
- Varun Gupta
- March 30, 2020 22:13
1 vote 4 comments
mutect2 multi-sample Answered
- zhao shilin
- May 07, 2020 17:27
- Edited
0 votes 35 comments
What does RAW_MQ annotation mean ?
- Robert Baldwin
- July 27, 2022 19:49
0 votes 3 comments
Can't access google cloud it says permission required
- HQ Zhao
- October 27, 2022 02:03
0 votes 2 comments
Report file CreateExtendedIlluminaManifest Report file
- James Gallant
- October 31, 2022 15:28
1 vote 1 comment
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
Picard CollectHsMetrics output
- Giovanni Cerchia
- July 21, 2022 12:29
0 votes 3 comments
Issues with LiftoverVcf Answered
- Mohammad Deen Hayatu
- October 06, 2022 06:43
0 votes 6 comments

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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.