New User Advice

Unable to unzip GATK
- Giang Tran
- October 12, 2024 03:38
0 votes 4 comments
A USER ERROR has occurred: Input files reference and reads have incompatible contigs: Found contigs with the same name but different lengths:
- Danielle Becker
- September 29, 2024 21:10
0 votes 5 comments
GATK Germline CNV calling
- Ramesh
- August 26, 2024 16:16
0 votes 8 comments
Funcotator Error. WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant.
- Anthony Pompetti
- January 23, 2024 18:21
- Edited
0 votes 2 comments
Collecting alignment metrics at READ_GROUP level with Picard
- Edward Formaini
- September 20, 2024 04:37
0 votes 4 comments
Using CrosscheckFingerprints (Picard) on mice RNAseq data
- Kaoutar Abaakil
- September 18, 2024 13:00
- Edited
0 votes 1 comment
GATK Installation MS windows 11
- Dhanush Tummala
- September 19, 2024 15:18
0 votes 1 comment
Comprehending Duplicates in Mutect2 and filtering
- Kate Newcomer
- August 20, 2024 20:53
0 votes 2 comments
MergeBamAlignment :: Unable to load libgkl_compression.so with GATK 4.4.0 and 4.6.0
- Gabdiel E Yulfo-Soto
- September 11, 2024 16:47
0 votes 2 comments
Tumor-match mode doubt
- Paulo Ricardo
- August 22, 2024 13:20
0 votes 1 comment
Base Quality Score Recalibration doubt
- Paulo Ricardo
- August 20, 2024 09:43
- Edited
0 votes 4 comments
Picard CollectHSMetrics: how do mean_coverage; max_coverage and min_coverage get calculated when using --PER_TARGET_COVERAGE option?
- Monica Della Rosa
- August 16, 2024 13:41
0 votes 4 comments
Running GenomicsDBImport/CombineGVCFs on Azure leads to User Error: Illegal argument value
- Martin Danner
- April 18, 2023 10:29
- Edited
0 votes 2 comments
Tumour Match Mutect
- Paulo Ricardo
- July 01, 2024 15:41
0 votes 1 comment
Error in MarkDuplicates
- Nahdia Afiifah Abdul Jalil
- April 03, 2024 12:23
0 votes 2 comments
Creating PON
- Paulo Ricardo
- July 01, 2024 11:34
0 votes 2 comments
Germline Variants Calling
- Paulo Ricardo
- June 25, 2024 11:14
0 votes 5 comments
GenomiCDBImport issue
- RN Sarma
- June 17, 2024 05:00
0 votes 9 comments
gatk4.5 markduplicatesspark error spark
- Ryan Welch
- June 20, 2024 21:09
0 votes 4 comments
How to apply VQSR to mouse samples, to find the best thresholds for hard-filtering
- Paulo Ricardo
- June 19, 2024 15:30
0 votes 4 comments
VariantFiltration isn't working
- Paulo Ricardo
- June 20, 2024 14:12
0 votes 1 comment
Contig names lost after FastaAlternateReferenceMaker
- Kheira BOUZID
- May 15, 2024 09:28
- Edited
0 votes 4 comments
Help with WDL workflow for mutec2? Answered
- Alex Lee
- July 14, 2021 17:01
0 votes 9 comments
One normal sample. Do I create a panel of normals? I want to run tumor-only mode, in mouse samples
- Paulo Ricardo
- June 09, 2024 11:00
0 votes 4 comments
gatk genome loc coordinates exceed the contig size. While trying to run genomicsdbimport
- Paulo Ricardo
- June 09, 2024 09:43
0 votes 4 comments
Checking of GATK script
- RN Sarma
- June 07, 2024 08:09
0 votes 1 comment
GATG-4.8
- RN Sarma
- June 06, 2024 11:48
0 votes 1 comment
BQSR error
- Tanya Sarkin Jain
- May 13, 2024 18:43
- Edited
0 votes 4 comments
Joint Call on individuals sequenced with differing coverage
- Phoebe
- May 09, 2024 08:34
0 votes 2 comments
mutect2 analysis with one tumor vs two normals from the same individual?
- María Fernanda Talavera Cruz
- May 02, 2024 02:27
0 votes 3 comments

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