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REMS needed to allow Applicant to apply for permissions to resources that are more fine-grained than the current atomic "resource" (such as, dataset). For instance, applicants want to get access to at…
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Update the `dtype` of `rsid`, `chrom`, and `genotype` columns to be `pandas.StringDtype` as recommended [here](https://pandas.pydata.org/pandas-docs/stable/user_guide/text.html#text-data-types).
Al…
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Hi -
I've gotten the tool up and running and it seems to be working well. However, I am trying to understand how well my genotypes are defined/separated. How can I do so? I tried to recreate the c…
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We would like to verify whether there is a significant difference in efficiency of the hm pipeline for seq GWAS.
1. Calculate the average % of dropped and unable to harmonise variants among a repres…
ljwh2 updated
5 months ago
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Multi-allelic variants where introduced in #17 by adding a new `List` with the secondary alternates. This approach has some problems for mixtures of SNPs and INDELs when the normalization changes the …
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## input files
would be nice if we could support the following inputs
- [x] Path objects representing paths to the files
- [x] and files ending in gz
- [x] `sys.stdout` and `sys.stdin`
-…
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It appears that TOPMed has changed the format of the info files it produces. For example, rather than a single Genotyped field, there are now two fields, IMPUTED and TYPED. Do you plan to update the…
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(creating a separate issue for this, as #124 appears due to something else)
One potential issue could be if inconsistent choice of reference alleles in sumstats, LD file and genotype file isn't res…
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Hi, I have regenotyped 9000+ samples and gotten a small set of 72 samples with all genotype (GT) results to unknown (./.)
The other 9000 samples have around 2400 structural variant (SV) which are …
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```SQL
SELECT s.uniquename AS stock_fbid,
s.description AS stock_name,
f.uniquename AS feature_fbid,
f.name as feature_name
FROM stock s
JOIN stock_genotype sg on s.stock_id=sg.stock_id
…