User: timothy.delory

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Posts by timothy.delory

<prev • 5 results • page 1 of 1 • next >
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LD Complete lookup table problem
... Hello bioinformatics people, I am using the complete option of LDhat. I understand it is supposed to take days possibly to run the LDhat complete command, and mine (split 20 ways) are finishing in about 5 minutes. When I run on our SLURM I don't get any explicit errors from ldhat itself, but my wor ...
pop_gen ldhat ld written 1 day ago by timothy.delory0
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Comment: A: GATK AnalyzeCovariates No improvement/Sequencing Bias Removal
... https://ibb.co/8DD6PYP here is the URL to the image of the Analyze Covariates plots. ...
written 3 months ago by timothy.delory0 • updated 3 months ago by genomax91k
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GATK AnalyzeCovariates No improvement/Sequencing Bias Removal
... I used the GATK bootstrap method to re-score my quality scores/eliminate systematic biases for my population genetic dataset in a non-model organism. However my "after" score doesn't improve at all from the before. The GATK best practices suggest running until you converge; my data have converged, w ...
gatk bqsr written 3 months ago by timothy.delory0
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Comment: C: Snakemake Error (incorrect wildcard use)
... Thank you. This was helpful to me! I added in the expand option as well. ...
written 6 months ago by timothy.delory0
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Snakemake Error (incorrect wildcard use)
... I am trying to run a simple snakemake rule for a basic bwa mem on several paired end reads. I am getting the error: > Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards. However, my rule inputs and outputs are structured much like the bwa example ...
software error snakemake written 6 months ago by timothy.delory0

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