GATK download link not working?
I'm trying to download GATK to no avail. I created an account, signed in, accepted the license agreement, and then I click the download button. This takes me to...
View ArticleParameter "--fraction_contamination" does not work in Mutect-1.1.7
hi, I used Mutect-1.1.7 to call low frequency variants, and I want to set "--fraction_contamination" to be 0. But it seemed that can't work. I got the message "--fraction_contamination: command not...
View ArticleASEReadCounter Empty Output
I am using ASEReadCounter on RNA seq data. I have followed the steps of the RNA seq best practices. When I run ASEReadCounter, I get no warnings, but the output CSV file is empty other than column...
View ArticleClik here to view.
(How to) Map and clean up short read sequence data efficiently
If you are interested in emulating the methods used by the Broad Genomics Platform to pre-process your short read sequencing data, you have landed on the right page. The parsimonious operating...
View ArticleWhat are the standard resources for non-human genomes?
We're trying to put together some recommendations for folks who want to use GATK tools on non-human genomes. But we really don't have much experience with non-human genomes, so we're hoping that those...
View ArticleWhat does MuTect output means?
Hello! Currently, I am working on identification of somatic mutations on exome data. For this, I am using the combination of GATK + MuTect2 using following code: java -jar...
View ArticleDepthOfCoverage and DP reported on VCF
Hi, I have noticed some inconsistency between the read depth reported from the DepthOfCoverage tool, and the DP fields in VCF. I am wondering if anyone can help me understanding how it works. I am...
View ArticleMany reference reads found with GQ=0 and cannot be visualized
Dear GATK Team, I've seen a phenomenon that I've been struggling to explain: Using HaplotypeCaller, at one particular locus, there seems to be 192 reference reads, however, the GQ is zero, with the...
View ArticleERROR MESSAGE: Unknown file is malformed in DepthOfCoverage
Hi there, I am using DepthOfCoverage to get the exome coverage of a target reference and getting this error. ERROR MESSAGE: Unknown file is malformed: Could not parse location from line: chr1 11873...
View ArticleVariant Calling by Unified Genotyper
I am using GATK version 3.6 tool Unified Genotyper for variant calling in pooled data set but I am unable to detect mutation in positive control, but when I used GATK 3.5 Unified Genotyper, I am able...
View ArticleUnifiedgenotyper walker not found
When i run GATK i get this error ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.6-0-g89b7209): ERROR ERROR...
View ArticleUsing Genome STRiP with SLURM instead of LSF
I'm trying to use the most recent release of Genome STRiP for CNV calling, but my cluster doesn't use LSF. As a result, I'm getting following error all over the place: ERROR 17:15:10,412 QGraph -...
View ArticleGATK Workshops World Tour 2016
For the last few years, we have taught GATK workshops at institutions in various countries around the world. It started out as a small-scale effort with one or two workshops a year in addition to the...
View ArticleFastaAlternateReferenceMaker -- how does it deal with the '*' deletions.
Hi GATK best team, I am having a question concerning FastaAlternateReferenceMaker once again. I was wondering in a case when there is an alternate 0/2 and that the options are A T,* what does the...
View ArticleError with HaplotypeCaller
I have a bam file with duplicates removed. And I added the read groups using picard as: java -jar gatk/picard-tools-2.5.0/picard.jar AddOrReplaceReadGroups \ I=input.bam \ O=input.group.bam \ RGID=4 \...
View ArticleThe error of Mark Dupplicate
I run the step of Mark Duplicate in the server, but it always print an error message even though I changed server. This is my input: java -jar /home/yangguoqian/biosoft/picard-tools-2.5.0/picard.jar...
View ArticleSAM bin field error for the GATK run
Hello, I am running Picard+GATK pipeline on paired-end illumina samples. The bam files were downloaded from TCGA. GATK 3.1.1 and java v1.7.0 were used. I have encountered such an error as below. I...
View ArticleFrequently Asked Questions
1. What does error message X mean? See the FAQ section on frequently encountered errors. 2. Can I use Genome STRiP to do discovery or genotyping in a single high-coverage individual? Genome STRiP is...
View ArticleEMIT_ALL_SITES in HaplotypeCaller
If I run HaplotypeCaller with a VCF file as the intervals file, -stand_emit_conf 0, and -out_mode EMIT_ALL_SITES, should I get back an output VCF with all the sites from the input VCF, whether or not...
View ArticleNon-human truth and training resources
Good day, I'm working on a bird whole genome and I need to set up truth and training resources. In the documentation it says the following and I just want to confirm that I understand this correctly:...
View Article