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Would be great if could make the cached clumping use less memory.
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Hi,
For strategy 2, you recommend subsetting the donor VCF file as below. Specifically how would you recommend to filter out SNPs with "too much missing values" or "genotypes too similar across don…
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Hi,
My issue is similar to https://github.com/sanger-pathogens/snp-sites/issues/96 only that when I manually look at the alignment file, I can find many mutations. The attached file is one such examp…
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hello, Yao Nan!
I have been inspired by your recent work, and I've been examining the paper and the scripts you've provided. However, I've encountered a difficulty in the script **diploid_selfing_SNP…
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I just got this running
Note that:
MAF is not inferred even though I am passing Freq col, and I am seeting maf to calculate
## Code
```
columnsnames = echodata::construct_colmap(munged= FAL…
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Need to add tests that specifically test the HG38 flows.
Should add in a set of representative unit tests that span the large normal data set.
Check new contigs as well.
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Hi,Sorry to bother you @Fnyasimi. when I used the sample data(cad.add.160614.website), I found that the results of harmonization(**Harmonization, not Quick Harmonization**) and imputation were the sam…
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How can I translate my .gds into .ped and automatically taking the family information from my gds object which I added before with add.gdsn() ?
Such as from:
+ [ ]
|--+ sample.id { Str8 173…
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Hi Dr. Cheng,
I hope this message finds you well. I'm Yihe Yang and I greatly appreciate your work on MR.CUE. In my simulations, I've found that MR.CUE and the univariable version of MRBEE (as des…
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I see this error in the host dmesg logs, and my VM failed to boot. This seems to be intermittent and sometimes the VM works and sometimes it doesn't.
We are using the latest repo state as of frida…