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Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character
- Graeme Thorn
- May 27, 2022 21:05
- Edited
0 votes 0 comments
Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
- Senwei
- April 27, 2022 07:59
1 vote 2 comments
Cromwell metadata of huge workflows
- Rafal Gumienny
- April 07, 2022 12:24
- Edited
0 votes 1 comment
Genomestrip preprocessing error
- chae chae
- March 08, 2022 03:41
- Edited
0 votes 13 comments
change the memory when running SVPreprocess
- zzq
- January 11, 2022 06:21
- Edited
0 votes 2 comments
VariantsToTable positional argument eror
- Owen Hudson
- December 14, 2021 17:22
0 votes 1 comment
Dictionary cannot have size zero error
- Nish314
- November 20, 2021 00:20
- Edited
0 votes 1 comment
CNNScoreVariants carshes with java.lang.NullPointerException with Python 3.8 & JDK 1.8
- KUMAR Chandan * TCS
- November 02, 2021 09:56
0 votes 1 comment
CalculateContamination 4.1.2.0 org.apache.commons.math3.exception.TooManyEvaluationsException
- 陈星瀚
- October 29, 2021 09:21
0 votes 1 comment
HaplotypeCaller inconsistency with different interval lists
- Gytis Mackevičius
- September 10, 2021 05:53
- Edited
0 votes 5 comments
My recalibration table from BaseRecalibrator is empty
- Calum Tattersfield
- August 25, 2021 18:14
- Edited
0 votes 5 comments
SplitNCigarReads does not seem to split reads properly as it was before 3.8-1?
- SkyWarrior
- June 21, 2021 13:29
- Edited
0 votes 7 comments
Running Genome STRiP SVPreprocess, but I got error message: "Invalid command line: Malformed walker argument: Could not find walker with name: ComputeInsertSizeHistogramsWalker"
- Norio Tanaka
- June 15, 2021 14:22
0 votes 4 comments
GenomicsDBImport - A USER ERROR has occurred: Failed to create reader from file: 2.0
- Jared Johnson
- May 07, 2021 20:44
0 votes 1 comment
sample_gender.report.txt is empty when running SVpreprocess restricted to chromosomes
- zzq
- April 16, 2021 11:52
- Edited
0 votes 8 comments
How do I keep a glob from copying a file in Cromwell / WDL
- Gregory Dougherty
- March 09, 2021 00:24
0 votes 1 comment
How to Fix the follow ValidateSamFile error ?
- Luis Enrique Romero Cruz
- March 06, 2021 03:51
0 votes 1 comment
BaseRecalibrator on MT .bam files
- Sharon Cox
- February 19, 2021 09:48
- Edited
0 votes 1 comment
LiftoverVcf: hg19 to hg38 all variants mismatched
- Ken Hanscombe
- February 17, 2021 14:13
0 votes 3 comments
Error when trying to generate the second recalibration table for AnalyzeCovariates
- ISmolicz
- February 17, 2021 12:03
0 votes 10 comments
Checking ReadGroup name in BAM file with GATK instructions
- Julianne Radford
- February 16, 2021 19:04
0 votes 1 comment
How to work with CNN variant caller
- Danio Rerio
- February 16, 2021 16:09
0 votes 3 comments
HaplotypeCaller and Read Group Errors
- Julianne Radford
- February 11, 2021 17:45
0 votes 1 comment
DepthOfCoverage Error: Refseq file contains transcripts with zero coding length
- ashgorden
- February 04, 2021 08:15
0 votes 2 comments
filterSamReads stdout format error
- rcorbett
- February 04, 2021 15:31
- Edited
0 votes 15 comments
Cromwell stuck at WaitingForReturnCode on Mac
- Marc Crepeau
- February 01, 2021 21:00
0 votes 3 comments
Reference Fasta vs Alt Reference Fasta
- Linda Do
- January 29, 2021 21:56
0 votes 2 comments
HaplotypeCaller -ERC GVCF -variant_index_type LINEAR
- Matilde
- January 22, 2021 18:22
1 vote 1 comment
Why do I see difference in ploidy in GT field within same sample after GenotypeVCFs
- Emila Mańko
- January 21, 2021 17:54
0 votes 3 comments
Comparison between ReadsPipelineSpark and MarkDuplicates
- AMN
- January 20, 2021 00:36
- Edited
0 votes 7 comments

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