User: steve

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Posts by steve

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Comment: C: Samtools problem with running (Conda)
... No, definitely a full dedicated installation. Its only wasteful if you care about disk space. Its a much more portable and reproducible method than just assuming the target system will have a compatible conda version already installed. Almost like a self-contained Docker replacement minus the requir ...
written 5 days ago by steve2.0k
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Comment: C: Samtools problem with running (Conda)
... > Avoid directly using conda install as much as possible A nice workaround to this is to just have a dedicated conda installation for every software stack, and keep the entire installation saved in a script for reproducibility :) [Example here](https://github.com/stevekm/toolbox/blob/b03c4d2cfd6 ...
written 7 days ago by steve2.0k
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Answer: A: Samtools problem with running (Conda)
... I have had issues with `ncurses` giving similar errors with other programs, the solution was to install `ncurses` from the conda-forge channel *before* installing the rest of the dependencies; conda install -y conda-forge::ncurses conda install -y -c bioconda samtools Maybe give this a sho ...
written 7 days ago by steve2.0k
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Comment: C: Experience running Nextflow based pipelines on an on-premise Kubernetes cluster,
... Also you may want to check the Issues page on GitHub for Kubernettes related listings; https://github.com/nextflow-io/nextflow/issues Also you can check out the Gitter chatroom; https://gitter.im/nextflow-io/nextflow ...
written 12 days ago by steve2.0k
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Comment: C: Experience running Nextflow based pipelines on an on-premise Kubernetes cluster,
... I have never used Kubernetes but I have been using Nextflow + Singularity extensively for a while now. I have had no issues with its stability, it has been far more stable than the HPC system that we run it on; almost all of our pipeline failures are attributed to underlying system failures outside ...
written 12 days ago by steve2.0k
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Comment: C: Export Coverage on IGV
... sounds like you might want to create a BigWig file? Also might want to look at GATK DepthOfCoverage (https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php) ...
written 15 days ago by steve2.0k
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Safe ways to chunk data to speed up Pindel?
... I am trying out Pindel (https://github.com/genome/pindel) with our exome data, and even on demo datasets it is taking extremely long to run, way longer than is feasible in a production setting. Using Pindel version 0.2.5b9, 20160729, running in Singularity container on our HPC cluster. My config fil ...
indel pindel written 15 days ago by steve2.0k
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Comment: C: Best practice for serial variant calling
... if your plasma samples were collected independently then I think you would definitely want to run the variant calling independently for each tumor-normal pair. They would be considered separate biological samples. ...
written 15 days ago by steve2.0k
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Comment: C: Best practice for serial variant calling
... not sure about "best practice" but I generally run all the variant calling per-sample or per-pair in parallel, then convert to .tsv with GATK VariantsToTable, add sample labels to the .tsv, then concatenate the .tsvs into a single table for review. If you have tumor-normal pairs then be sure to use ...
written 16 days ago by steve2.0k
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Comment: C: Somatic indel calling with Pindel
... thanks for this, exactly what I was looking for ...
written 18 days ago by steve2.0k

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