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Hi,
I'm trying to use bcbio in a virtual machine where the windows host only has 8g of memory. The project is a 16 sample WES experiment. I've allocated 6g to the guest OS (biolinux 8). I left bcbio r…
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@jzook said in #4:
> In terms of prefiltering, my one concern with this is where part of a complex variant is excluded by the bed file in one representation and included in another representation. …
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In light of Brad's old blog post on FreeBayes performance without the need of BQSR and local indel realignment, I'm wondering whether these steps should be kept, or skipped unless the quality is reall…
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From clinvar, using CLNDBN as disease name and GENEINFO as the genes, we can populate the the clinvar_disease column with a | delimited list of diseases that match the current variant's top_impact.gen…
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jjgao updated
9 years ago
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Ported from [cycledash #546](https://github.com/hammerlab/cycledash/issues/546)
I see that error message frequently, don't know what it means, and don't know what if anything I can do to fix/work aro…
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This is a feature request; I'd appreciate it if the annotated Chanjo coverage BED file could be part of the final `upload` results. I am referring to an unfiltered (!) version of the temporary BED fil…
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Thanks, @roryk, for setting up `sailfish`. However, it appeared to me that it isn't a complete replacement for `express` yet since you are taking the input fastqs rather than the transcriptome-aligned…
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A post-doc who is setting up a new bioinformatics lab asked, "Where should I store the data?" Right now, her group has samples in a freezer and sequence data from them archived on a couple of portabl…
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I am attempting to run a local workflow mirroring `run-PopSV-local.R` from the `scripts` folder. I am using a small sample of bam files to learn the package and make sure I can run everything. When ru…