Other

jar for mutect 1.1.7
- Knight Ni
- April 19, 2020 17:08
1 vote 6 comments
Panel of Normals Documentation Answered
- Ryan Gimple
- April 16, 2020 17:48
1 vote 16 comments
Cromwell GATK json list of files
- Kristian Unger
- April 16, 2020 07:41
0 votes 3 comments
some Mito-mutations can't detected out right from amplicon data using Mutect2
- rime
- April 13, 2020 05:46
0 votes 2 comments
problem with output from combinegvcf gatk 4.1.3
- flaviarogerio
- April 12, 2020 13:23
0 votes 1 comment
Mutect2-exome-panel.vcf Not Found
- Ryan Gimple
- April 11, 2020 20:03
0 votes 3 comments
GATK Runtime Error 3.8
- Nicholas Cho Rui Wen
- April 09, 2020 10:35
0 votes 5 comments
multiple vcf files in FastaAlternateReferenceMaker
- mk
- April 09, 2020 04:59
0 votes 3 comments
VariantFiltration Invalid Argument
- mons7re
- April 08, 2020 10:57
0 votes 3 comments
GATK/Picard does not detect mates in paired-end BAM
- jipvdinter
- April 07, 2020 11:34
- Edited
1 vote 3 comments
GenotypeGVCFs: unexpected output in PGT and PID fields
- Johnny Li
- March 31, 2020 21:35
- Edited
0 votes 3 comments
picard test compile error
- Kelly Swarts
- March 30, 2020 19:34
0 votes 1 comment
FilterByOrientationBias vanished in 4.1.6.0
- riederd
- March 30, 2020 11:41
0 votes 11 comments
GenotypeGVCFs: java.lang.NullPointerException
- Anze Staric
- March 30, 2020 11:28
0 votes 9 comments
GenomeSTRiP ReciprocalOverlapAnnotator Annotation track not sorted
- Asma Riyaz
- March 29, 2020 21:34
- Edited
0 votes 8 comments
Error using a edited gatk wdl (bam-unmapped-bam workflow) to accept array[files] as input rather than a single .bam file
- sahuno
- March 28, 2020 19:11
0 votes 3 comments
Genome STRiP CNVDiscovery pipeline error
- Beilei Bian
- March 25, 2020 00:39
0 votes 27 comments
Custom ReadFilter to ignore malformed reads ?
- Yokofakun
- March 21, 2020 13:26
0 votes 2 comments
Picard ExtractIlluminaBarcodes return NullPointerException error
- Jing Lin
- March 20, 2020 21:52
0 votes 4 comments
GATK4 HaplotypeCaller - read is malformed
- Yi-Sian Lin
- March 19, 2020 05:21
- Edited
0 votes 2 comments
Getting CNNScoreVariants to run faster
- WVNicholson
- March 18, 2020 16:29
0 votes 3 comments
Broken GATK 3 documentation links
- Harly Durbin
- March 16, 2020 19:18
0 votes 1 comment
HaplotypeCaller bam file path not recognized
- Phillip Morin - NOAA Federal
- March 13, 2020 18:42
0 votes 7 comments
I want to know sequence_group_intervals in fivedollar-genome-anlalysis pipeline
- BI_joy
- March 11, 2020 08:53
- Edited
0 votes 1 comment
Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?
- mk
- March 11, 2020 00:37
0 votes 4 comments
Dockerfile for genomes-in-the-cloud
- Tony Bendis
- March 10, 2020 05:16
0 votes 5 comments
error java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Byte
- BI_joy
- March 02, 2020 12:16
0 votes 1 comment
CreateSomaticPanelOfNormals fails
- Dieter Best
- February 28, 2020 23:46
0 votes 2 comments
Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH
- Jose Arcadio Buendia
- February 28, 2020 01:53
- Edited
2 votes 2 comments
Why does my vcf contain a genotype when there are no reads supporting it?
- Jeff Duty
- February 27, 2020 14:51
- Edited
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.