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This is an example from drprg, Michael's data. Pandora discover and map output here: `/hps/nobackup/iqbal/mbhall/drprg/paper/results/amr_predictions/drprg/illumina/PRJNA436454/SAMN08626350/SRR6824314`…
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Most Affymetrix URLs are broken since now moved to https://www.thermofisher.com/.
It looks like they're still going to call it Affymetrix Arrays, cf. https://www.thermofisher.com/us/en/home/life-sc…
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We are interested in using pypgx to call star alleles, but (in one scenario) we do not want to report star alleles that have Unknown or Uncertain function. For example, if a sample was called CYP2D6 *…
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Chris and Sangtae;
This is a follow-up to a bcbio discussion (https://github.com/chapmanb/bcbio-nextgen/issues/2112#issuecomment-338307641) which I thought could use it's own thread. In bcbio we're c…
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Hi,
Would you be interested in supporting genotyping from remote cram files? I noticed it only requires to comment out two lines at
https://github.com/gymrek-lab/LongTR/blob/d9323818eea55cbf55ac72…
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GATK has implemented a (quite radical) new way of encoding missing data, that we will need to support going forward:
https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531
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* **Do you want to request a *feature* or report a *bug*?**
feature
* **What is the current behavior?**
reporter.BadOutsideCallException when outside CYP2D6 genotype call is an invalid fo…
songx updated
2 months ago
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In http://biccsrv3.epfl.ch:32786/check_pheno
We need to add the new GWAS calculation.
Also, we need to add the gene enrichment results.
We have two options:
- 1. Keeping it within the main R scr…
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HWE (x)
association testing
Ne
parentage
genomic prediction
manhattan plots
SFS
abc
plots with circos
abba/baba
plotting on maps (pop assignments, ect).
assignment (fastStructure calls and …
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## Describe the issue
We continue digging into differences (https://github.com/Ensembl/ensembl-vep/issues/1031) caused by `--no_stats` workaround from https://github.com/Ensembl/ensembl-vep/issues/81…