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We have discussed development of a credible set planning page within our merged product.
Please see here for current [study-locus page in OTG for reference.](https://genetics.opentargets.org/study-lo…
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https://github.com/jdalapicolla/LanGen_pipeline_version2/blob/d98a65e128e810a39b516a9dac40eaae48b856de/1.1_FILTERING_SNPs.R#L316-L317
Hello Jeronymo. Thank you for your previous help.
How did yo…
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This ticket keeps track of existing eQTL fine mapping methods -- please use new comment for additional references so that I can be notified to add here and to my mendeley:
1. Davis, Joe R., et al.…
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Expected Behavior
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After a genotype upload, need to verify that everything is correct in the database.
By nd_protocol o…
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bash snphylo.sh -H FINAL-ADMIXTURE-CVC880-MandSatsumaClem-CVC97-TASSEL-Samplename.hapmap.txt -b -a 9 -l 0.2 -m 0.1 -M 0.1 -P CVC97
Start to remove low quality data.
91 low quality lines were remov…
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Some variants in SeqArray gds files can have multiple alternate alleles. I looked into how the LD functions behave with multiallelic variants using the example file in [analysis_pipeline](https://gith…
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Hi Pierre,
Thanks for the developing this package. I have found it really useful for cluttering epigenetic and genetic data.
I am currently applying it to large-scale SNP data. I had an issue …
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Output from pdf2text transform (from norma) is reasonable but not brilliant. It's also quite slow tbh.
Given pdftotext (Poppler) is already pre-installed in the workshop VM, perhaps better just to cal…
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The file `R/phasingImpute4.R` has the comment
`## impute for chrX PAR >> with an additional flag: --Xpar.`
However, the lines following it and running IMPUTE4 do not have that flag set, i.e.
…
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@Hua-Zhou at #58
> We may open another issue regarding LD pruning of SNPs so that remaining
SNPs are not very highly related. A literature review of how Plink does it
is helpful.