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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!
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How to include non variant sites in the output vcf of GenotypeGVCFs?
Samwittwer
Zurich, SwitzerlandMember ✭
Hello
I'd like to include confident non variant sites in my downstream analyses. If I understand correctly, this was possible in previous versions with --includeNonVariantSites but I'm not seeing an option that allows me to do this in GATK4. Am I missing something obvious or is this currently not possible?
Thank you very much in advance and best wishes
Sam
Tagged:
Best Answer
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Sheila
Broad Institute admin
@Samwittwer @davee
Hi Sam and Dave,This is currently not possible in GATK4, but there are plans to implement it. You can keep track of the status here.
-Sheila
Answers
I would also be interested in knowing the answer to this. Is it possible to include non-variant positions in the output of genotypeGVCFs using GATK4?
Thanks,
Dave
@Samwittwer @davee
Hi Sam and Dave,
This is currently not possible in GATK4, but there are plans to implement it. You can keep track of the status here.
-Sheila
Hi @Sheila
Thanks for the info. I'll be sure to follow that ticket for updates.
Best,
Dave
Hi @Sheila,
Do you konw when the --includeNonVariantSites option will be avalible for GATK4? My colleagues and I are in urgent need of this function.
@jiykun
Hi,
I am not sure when the team will get to this, but it is flagged as high priority. I will remind the team about this.
-Sheila
I'm wondering if in this time, the option "Include non variant sites" in the output vcf of GenotypeGVCFs is already available?
If not, someone could me give a tip how I can do that using another way?
@flaviarogerio Based on this release, this option is now live! You can always check back at that link for any further information on releases. Additionally, here is a post that lists some ideas for a workaround if you wanted to try other methods as well.
Dear GATK Team,
I was wondering what is the exact meaning of "." in GenotypeGVCFs? If it is related to the low or no call, what do you mean by low or no call then? For example, does GenotypeGVCFs distinguish between a gene absence or a gene with low quality of calling? Or in both cases, this will be shown by "."?
Thanks in advance,
Negin
Any answer, please?
Hi,
The GATK support team is currently primarily focusing on resolving questions about GATK tool specific errors or abnormal results from the GATK tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and the tools.
We cannot guarantee a reply, however we ask other community members to help out if you know the answer.
For more information:
https://software.broadinstitute.org/gatk/blog?id=24419
https://gatkforums.broadinstitute.org/gatk/discussion/24417/what-types-of-questions-will-the-gatk-frontline-team-answer/p1?new=1