Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
problem in UnifiedGenotyper
mahyarhey
BostonMember ✭
I run the UnifiedGenotyper with 3 samples. After almost 4 hours I got the following ERROR. What is this error mean? How I can to fix the problem? Thanks
ERROR ------------------------------------------------------------------------------------------ ERROR A GATK RUNTIME ERROR has occurred (version 2.2-4-g4a174fb): ERROR ERROR Please visit the wiki to see if this is a known problem ERROR If not, please post the error, with stack trace, to the GATK forum ERROR Visit our website and forum for extensive documentation and answers to ERROR commonly asked questions http://www.broadinstitute.org/gatk ERROR ERROR MESSAGE: -1 does not represent a valid base character
Post edited by Geraldine_VdAuwera on
Tagged:
Answers
Hi Mahyar,
Can you please post the full stack trace? The stack trace is the part of the console output that details the problem, just before the ERROR block.
Hi Geraldine,
Unfortunately, I deleted the log file.
Then I'm afraid you'll have to re-run it. Try running with
-l DEBUG, it will give more information about what is wrong. Be sure to save the log file, as I can't do anything without that information.Hi Geraldine,
I run the UnifiedGenotyper for my all 42 samples and I got the VCF file for all sites. In the 4th column of the VCF file I have QUAL-value which is range between 0 to 25000. What would be the threshold of selection QUAL. (e.g. 50, 100, 1000, etc). Please advise>thanks
Please read the Best Practices documentation > http://www.broadinstitute.org/gatk/guide/best-practices
Hi Gerladine, I Used "HaplotypeCaller" for calling variant of one of my Bam file. However, after 3 hours it created the VCF file, but there is no information in the file and just heading. In below, you can see my commands: What is wrong? please advise, Thanks
java -jar GenomeAnalysisTK-2.2-4/GenomeAnalysisTK.jar
-R ucsc.hg19.fasta
-T HaplotypeCaller
-I 15V_post_reorder_GROUP.rg.bam
--dbsnp dbsnp_137.hg19.vcf
-gt_mode GENOTYPE_GIVEN_ALLELES
-out_mode EMIT_ALL_SITES
--out 15V_post_afterQC.vcf
Hi @mahyarhey,
For one thing, you set HC to genotype given alleles, but didn't provide any alleles. That doesn't explain why you have no output though -- did the run complete without error? It can be helpful to post the output log.