
ikeoluwao_o
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Activity overview
Latest activity by ikeoluwao_o-
ikeoluwao_o commented,
Hi Jason Cerrato, No worries at all. I would very much appreciate your help with this as it's still not resolved.
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ikeoluwao_o commented,
Hi Jason Cerrato It was not created using the generate-sample-map workflow. It was created by manually putting together the sample names and corresponding paths. I don't have access to this workfl...
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ikeoluwao_o commented,
Hi Jason Cerrato I'm unable to provide access to this individual object given that this specific bucket access control is uniform and not fine-grained. I've copied the file to the same bucket as th...
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ikeoluwao_o commented,
Hi Jason Cerrato, Thank you for willingness to help. Here is the path: gs://55trios/JointGenotyping.hg19.wgs.inputs.json. I've provided access to you.
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ikeoluwao_o commented,
Hi Beri, Thank you for your response. The first option did not work but the second one did. Can I ask if it's okay to proceed with the use of the VCF output for variant annotation (VEP) or is the...
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ikeoluwao_o created a post,
Best Google Cloud Platform workflow for FASTQ to multi-sample VCF
I would like to run 150 WGS samples through the GATK Best Practices workflow on Google Cloud Platform and have found that many of the workflows are optimized for hg38. Is there a way to use b37 ins...
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ikeoluwao_o created a post,
Error on Google Cloud Platform: Failed to evaluate 'gvcf_paths' in Joint Genotyping
I'm running gatk-workflows/gatk4-germline-snps-indels on the Google Cloud platform. I'm implementing the JointGenotyping.wdl on 50 exome GVCF files from a Sentieon DNAseq_DNAscope run. I edited the...
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ikeoluwao_o created a post,
Error on Google Cloud Platform: Joint GenotypingWf interval file is larger than 128000 Bytes
Deciding to continue to the Joint Genotyping workflow from the Running GATK Best Practices Google tutorial, I came across the error below. The error has been addressed in a previous issue. The solu...
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ikeoluwao_o created a post,
Error on Google Cloud Platform: haplotypecaller-gvcf-gatk.wdl with make_gvcf = false
The gatk-workflows/gatk4-germline-snps-indels GitHub README says "However, for instances when calling variants for one or a few samples it is possible to have the workflow directly call variants an...
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ikeoluwao_o commented,
Hello, Thank you for your response. Yes, all the other stages prior to stage 12 completed successfully. I mistakenly overrode the contents of the file you're requesting by re-running the script. ...