Also, I think UKB should label those individuals carrying CHIP - there are some studies in which UKB data were used and the CHIP carriers have been found. I'm not sure how UKB can help on this matter.
I would take 2-3 months at best. I let product manager know since 3 weeks ago. They need to prioritize all the requests they got from users. I can check on their decision.
If the tool that you want is available as Docker image, I recommend you go with that route. I think this is highly likely for Mutect2.
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Hello Chai,
I am looking for a tool in UKB RAP to call somatic mutations on UKB data too. However it is not still in the tool library in UKB RAP. It would be my pleasure if you accelerate this procedure.
@Ra S? @Burcu Çevik? Thanks for the feedback. The Mutect2 app should come out in a few weeks. We got it working and pass the test, but would need a few more checking and also roll out in production update cycle.
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Permanently deleted user
Thank you for your response. I look forward to hearing come out this app.
Thank you for this app but I could not run the Mutectcaller. When I click to run, I select my project. However, when I open analysis input 3, I was not able to find bam file. I only have CRAM file and VCF file in my exome sequences folder in bulk data. I guess I don't have BAM file in my project. I am sharing screenshot of folders in Exome sequences which exist in my project.
I am wondering how I can find BAM file or generally how to run this app?
I see. This is our shortsight from user experience point of view. I have let our product team know about this issue.
In UKB RAP all the mapped/raw read data are in CRAM, not BAM. For now, you could have a step to change them to BAM first (using Swiss-army-knife) and use our workflow feature to direct those BAM as input of this app. The cost for compute should be the similar (or might be cheaper since you do conversion using CPU). You should remove those BAM after use though because the storage of them would be expensive.
I didn't do this research myself, so I could not comment on it. It might be good for you to ask this as a new question since only you, me, and @Burcu Çevik? would get notification on this thread.
@Ra S? @Burcu Çevik? The mutect app could now accept either CRAM and BAM . The change happens yesterday. If you run into difficulty before, please try again.
I tried to run with The Mutectcaller (Parabricks accelerated) but this app does not support somatic mutation analysis that I want to do. In my project, I want to build a Panel of Normals file (pon_vcf.gz) and then I want to calls somatic SNVs and indels using as input file this VCF file.
Currently we are not considering to make these apps available on UKB RAP because it's not the main use case for RAP, but I can pass on this request to product team. We could also check if our partner who developed Mutectcaller (Parabricks accelerated) app also have the app for panel building. If you have any feedback for Mutectcaller (Parabricks accelerated) app in general, feel free to share feedback, so they could use for future improvement.
I want to note that I can see app-gatk4_mutect2_variant_caller_and_filter from command line. Could you check if that works for you?
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I would very happy if you can pass my request. If GATK4 Builder app is not going to be available for UKB users, I can use a builder app by developed NVIDIA. I would suggest that Tumor-only mode with a panel of normals (PON) can be added to the Mutectcaller app. There isn't this mode in the version 4.0.0-2.
I'm sorry. I didn't quite understand your question.
x GATK4 Mutect2 Variant Caller and Filter (gatk4_mutect2_variant_caller_and_filter), v2.0.0
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Permanently deleted user
I'm sorry. I tried but I could not login via the command-line interface. If this tool is available for the UKB users, why can not I see this tool in the UKB tools library when I log in via the user interface?
Comments
32 comments
Not currently. What tool/analysis approach do you have in mind?
MuTect2 (GATK v4.1.4.0).
There is no matched tumor/normal sample in UKB. Would you run it without matched normal sample then?
I want to call Clonal hematopoiesis of indeterminate potential (CHIP) carriers.
I see. That makes sense. I have let the team know that there is an interest to have this tool on the platform.
Also, I think UKB should label those individuals carrying CHIP - there are some studies in which UKB data were used and the CHIP carriers have been found. I'm not sure how UKB can help on this matter.
I think the best way is to send request directly to UKB to have CHIP as one pheno field. Then we can release it with subsequence pheno data update.
I'm wondering how long we should wait for the DNAnexus to implement MuTect2?
I would take 2-3 months at best. I let product manager know since 3 weeks ago. They need to prioritize all the requests they got from users. I can check on their decision.
If the tool that you want is available as Docker image, I recommend you go with that route. I think this is highly likely for Mutect2.
Hello Chai,
I am looking for a tool in UKB RAP to call somatic mutations on UKB data too. However it is not still in the tool library in UKB RAP. It would be my pleasure if you accelerate this procedure.
The product manager is already on it, but if you like to share more info about use case, that could accelerate the priority as well.
I am so pleasure to share more info about my study. I have an approved project. https://www.ukbiobank.ac.uk/enable-your-research/approved-research/a-uk-biobank-longitudinal-study-of-clonal-haematopoiesis-and-risk-of-alzheimer-s-disease In the context of this project, I plan to detect somatic mutation in genes involved in hematological malignancies. I am planning detect somatic CHIP variants with GATK Mutect2 using WES data in my determined cohort.
@Ra S? @Burcu Çevik? Thanks for the feedback. The Mutect2 app should come out in a few weeks. We got it working and pass the test, but would need a few more checking and also roll out in production update cycle.
Thank you for your response. I look forward to hearing come out this app.
@Ra S? @Burcu Çevik?
The Mutect app is now available.
https://ukbiobank.dnanexus.com/app/pbmutectcaller_ukb
Hi @Chai Fungtammasan?
Thank you for this app but I could not run the Mutectcaller. When I click to run, I select my project. However, when I open analysis input 3, I was not able to find bam file. I only have CRAM file and VCF file in my exome sequences folder in bulk data. I guess I don't have BAM file in my project. I am sharing screenshot of folders in Exome sequences which exist in my project.
I am wondering how I can find BAM file or generally how to run this app?
I see. This is our shortsight from user experience point of view. I have let our product team know about this issue.
In UKB RAP all the mapped/raw read data are in CRAM, not BAM. For now, you could have a step to change them to BAM first (using Swiss-army-knife) and use our workflow feature to direct those BAM as input of this app. The cost for compute should be the similar (or might be cheaper since you do conversion using CPU). You should remove those BAM after use though because the storage of them would be expensive.
I'm just wondering what reference genome you're using to call CHIP carriers?
I didn't do this research myself, so I could not comment on it. It might be good for you to ask this as a new question since only you, me, and @Burcu Çevik? would get notification on this thread.
@Ra S? @Burcu Çevik? The mutect app could now accept either CRAM and BAM . The change happens yesterday. If you run into difficulty before, please try again.
Hello @Ra S? ,
We've recently added a version of mutect2 called MutectCaller from the Parabricks GPU accelerated genomic analysis software. Does that satisfy your needs?
Thanks Gary - yes that'a great news.
Hi {@005t000000149vjAAA}? ,
I tried to run with The Mutectcaller (Parabricks accelerated) but this app does not support somatic mutation analysis that I want to do. In my project, I want to build a Panel of Normals file (pon_vcf.gz) and then I want to calls somatic SNVs and indels using as input file this VCF file.
Is it possible for you to make the GATK4 Mutect2 Variant Caller and Filter (https://platform.dnanexus.com/app/gatk4_mutect2_variant_caller_and_filter)and GATK4 Somatic Panel Of Normals Builder (https://platform.dnanexus.com/app/gatk4_somatic_panel_of_normals_builder) apps in the DNAnexus tools library available for UKB users? These apps very appropriate to my study.
Currently we are not considering to make these apps available on UKB RAP because it's not the main use case for RAP, but I can pass on this request to product team. We could also check if our partner who developed Mutectcaller (Parabricks accelerated) app also have the app for panel building. If you have any feedback for Mutectcaller (Parabricks accelerated) app in general, feel free to share feedback, so they could use for future improvement.
I want to note that I can see app-gatk4_mutect2_variant_caller_and_filter from command line. Could you check if that works for you?
I would very happy if you can pass my request. If GATK4 Builder app is not going to be available for UKB users, I can use a builder app by developed NVIDIA. I would suggest that Tumor-only mode with a panel of normals (PON) can be added to the Mutectcaller app. There isn't this mode in the version 4.0.0-2.
I'm sorry. I didn't quite understand your question.
I mean that the app-gatk4_mutect2_variant_caller_and_filter should already be available. Could you check if you have access?
I can't see this tool in UKB tools library.
Can you see it from command line?
$ dx find apps --name "*mutect2*"
x GATK4 Mutect2 Variant Caller and Filter (gatk4_mutect2_variant_caller_and_filter), v2.0.0
I'm sorry. I tried but I could not login via the command-line interface. If this tool is available for the UKB users, why can not I see this tool in the UKB tools library when I log in via the user interface?
Sorry that you run into issue. I am honestly not sure too. I need to do some digging and will get back to you on this.
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