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
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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.