User: dganiewich

gravatar for dganiewich
dganiewich60
Reputation:
60
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Trusted
Location:
Buenos Aires, Argentina
Last seen:
3 days, 7 hours ago
Joined:
5 months ago
Email:
d*********@leloir.org.ar

Posts by dganiewich

<prev • 11 results • page 1 of 2 • next >
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Comment: C: CWL docker command user
... I just realized that you use the Github file and not the Docker image, maybe that is what I am doing wrong... I'll check and get back to you ! ...
written 3 days ago by dganiewich60
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Comment: C: CWL docker command user
... Hi Tom, thank you very much for your help! Indeed, I have stuggled a lot with bioinformatic stuff !! I'm sorry for my belated response, but I have yet not been able to make it work... Maybe there is something wrong with my importation of the dockerfile? Just to be sure, my new code has: #!/us ...
written 3 days ago by dganiewich60
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Comment: C: CWL docker command user
... Hi Tom! Sorry for the belated response. Here is the command line tool where you can see the docker container: #!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool baseCommand: - "gatk" - "MarkDuplicatesSpark" hints: DockerRequirem ...
written 10 days ago by dganiewich60
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CWL docker command user
... Hi! I am using CWL to run a program, and when I do cwl-runner tool.cwl tool_params.yml, the docker command has a --user=500:500 When I try running my tool, there is an id error that doesn't allow me to run it correctly (see https://gatkforums.broadinstitute.org/gatk/discussion/comment/59004#Comme ...
cwl-runner cwl docker written 14 days ago by dganiewich60 • updated 7 days ago by Tom250
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Answer: A: How to choose variants for viewing in IGV?
... Dear Martina, I believe the answer is as broad as the question... I guess you obtained a long VCF and don't know where to start. As a general approach, you can start from most probably associated with disease to less probable by prioritizing variants. You could look at the type of tumor you are w ...
written 17 days ago by dganiewich60
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Comment: C: Calculating TPM from featureCounts output
... Hi! From the link to the program for calculating fragment length I don't seem to find that exact metric. Instead, I found the read length and the insert length, do you use here insert as synonym of fragment? I understand that ideally only the insert is aligned and in that case they can be the same, ...
written 4 weeks ago by dganiewich60
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Answer: A: GATK4 Mutect2 variants IDs not shown
... Just in case someone encounters the same issue, it has been answered in: https://gatkforums.broadinstitute.org/gatk/discussion/comment/57540#Comment_57540 There is no way of populating the ID field with GATK4 Mutect2 as of today (03/29/19). Best, Daiana ...
written 11 weeks ago by dganiewich60
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Comment: C: CWL BWA-MEM RG fields from string parameters - use several input strings to gene
... woohoo! Thank you very much Tom! ...
written 3 months ago by dganiewich60
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Comment: C: GATK4 Mutect2 variants IDs not shown
... Hi Pierre! Thank you for your answer. The page you're referring to is deprecated, as it is the BETA version. The newest one unfortunately does not have the --dbsnp option... https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mut ...
written 3 months ago by dganiewich60
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GATK4 Mutect2 variants IDs not shown
... Hi everyone! I am a beginner using GATK, so bear with me please. I am trying to do my variant calling with GATK4 new Mutect2 (not MuTect2), using as --germline-resource the af-only-gnomad.hg38.vcf.gz from the GATK's bundle. The command is pretty much the same as seen in the tutorial: https://soft ...
gatk4 variant calling mutect2 written 3 months ago by dganiewich60

Latest awards to dganiewich

Scholar 17 days ago, created an answer that has been accepted. For A: GATK4 Mutect2 variants IDs not shown
Scholar 11 weeks ago, created an answer that has been accepted. For A: GATK4 Mutect2 variants IDs not shown

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