Need Help?

Search our documentation

Forum thread to discuss GATK Germline tools

Realign BAM getting stalled at a particular position for days
- Nitin Bhardwaj
- October 26, 2020 14:39
- Edited
0 votes 1 comment
How to work with large data set with: GenomicsDBImport
- Arye Harel
- October 26, 2020 06:33
- Edited
0 votes 1 comment
BQSR
- Rayz Ghimire
- October 23, 2020 01:03
0 votes 3 comments
Recommended parameters for GenomicsDBImport
- Arye Harel
- October 25, 2020 07:26
- Edited
0 votes 1 comment
What are the initial files required in order to go through the Data Preprocessing, Variant Discovery and IGV phases of Genomic analysis?
- Kountay Dwivedi
- October 21, 2020 15:52
0 votes 3 comments
Sampletracking workflow using picard
- Matthias De Smet
- October 21, 2020 11:51
0 votes 1 comment
Genome STRiP CNV Discovery pipeline error
- Thandeka
- October 20, 2020 13:15
0 votes 5 comments
Read groups
- Rayz Ghimire
- October 19, 2020 19:42
0 votes 4 comments
GenotypeGVCFs
- Anupriya Dalmia
- October 19, 2020 12:51
0 votes 1 comment
GenomicsDBImport error due to GZIP header
- Devishi Kesar
- October 19, 2020 01:46
0 votes 3 comments
GATK VariantFiltration produce the error message:java.lang.NumberFormatException: For input string: "0.667,0.333"
- Bingdi Liu
- October 15, 2020 23:41
0 votes 3 comments
Data pre-processing for variant discovery - BaseRecalibrator, vcf input?
- Arye Harel
- October 19, 2020 12:15
- Edited
0 votes 6 comments
Error when running HaplotypeCallerSpark
- Jeongmin Bae
- October 14, 2020 05:58
0 votes 5 comments
Error running gatk4-genome-processing-pipeline workflow
- Maria Akimenkova
- October 13, 2020 13:59
0 votes 9 comments
How do I use MarkIlluminaAdapters properly in combination with its metrics for new adapters other than Illumina standards?
- NawarDalila
- October 13, 2020 08:55
0 votes 5 comments
Variant calling in gene H19 disabled due to zero mapping quality
- sirian
- October 13, 2020 01:06
- Edited
0 votes 5 comments
haplotypecaller DP much lower than apparent coverage
- Mark Rose
- October 12, 2020 13:40
0 votes 9 comments
"htsjdk.samtools.SAMFormatException: Invalid GZIP header" in VariantRecalibrator
- zhaol
- October 13, 2020 14:17
- Edited
0 votes 16 comments
UnifiedGenotyper in GATK4
- Alex Sanchez
- October 11, 2020 04:48
0 votes 1 comment
Does the CN with LQ need to be deleted?
- termius
- October 10, 2020 07:19
0 votes 2 comments
HaplotypeCaller ReassignOriginalMQAfterIndelRealignment
- eblake
- October 09, 2020 20:38
0 votes 1 comment
other reference in BaseRecalibrator known-sites option
- BI_joy
- October 08, 2020 09:51
0 votes 3 comments
The gatk GenotypeGVCFs produced an error: java.lang.IllegalArgumentException: sequenceNames.size() != indices.length
- Bingdi Liu
- October 07, 2020 19:06
0 votes 9 comments
MarkDuplicatesSpark substantially slower than original
- Chris Miller
- October 07, 2020 14:48
0 votes 5 comments
Error: Unable to load libgkl_compression.so from native/libgkl_compression.so (No space left on device)
- Alex Sanchez
- October 07, 2020 05:56
0 votes 5 comments
VQSR - indel MQ zero variance and
- Manuela Bonetto
- October 06, 2020 16:43
0 votes 1 comment
How to obtain a BED file containing valid regions of the GATK output VCF for a sample?
- Asi
- October 02, 2020 12:04
0 votes 3 comments
Unable to perform variant filtration on GenomeSTRiP genotyped sites vcf
- Melissa Nel
- September 30, 2020 14:04
0 votes 5 comments
The gatk haplotypecaller cannot initialize the engine when I run my script or command on the same file again.
- Bingdi Liu
- September 30, 2020 05:55
0 votes 8 comments
The Future of CNN Tools
- micknudsen
- September 29, 2020 19:58
0 votes 2 comments

«
‹
1
2
3
4
5
6
7
8
9
›
»

Powered by Zendesk