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reprosteps: download prerequisites as described in http://localhost:8891/notebooks/gwas101.ipynb, then execute
```import os
from gwas_tools import read_bed, write_bed
os.system('plink2 --bfile chr2…
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- Plink2.0 has an option to output files in the [gwas-ssf standard format](https://github.com/EBISPOT/gwas-summary-statistics-standard)
- Not everyone is using plink to generate their files for submis…
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Hello and thanks for the work!
We've been looking at various association tools. Based on the code, it looks like PLINK2 computes the logistic regression model using a Cholesky decomposition method?…
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Both Relate and ARG-needle read data in "Oxford phased haplotype file" (.haps + .sample) format, as described at https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample (also s…
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### Description
I am trying to run plink2 on my MacBook Air. I downloaded plink2 from [here](https://www.cog-genomics.org/plink/2.0/) by selecting the download link for Alpha 5.14 final for macOS M…
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Every time I try to build 2.0, I get the error
```include/plink2_zstfile.h:32:12: fatal error: 'zstd.h' file not found```
I installed zstd as was recommended on a previous issue, but still get the…
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Hi,
In step 2 there's usage of a file:
plink2 ... --keep ~/Documents/biobank/ukb_phenotypes/indiv_filtered_v2.txt
However, the closest thing I can see for that file is at step 3 where the fil…
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Hi,
I have a project for homodimers study. And i want to identify the interaction interface of the dimer. So I did an experiment with 14N and 15N proteins (used in a 1:1 molar ratio) . I want to …
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I made a comparison between the PLINK2 glm result from the some range versus reading the dosage matrix with seqminer. The result from seqminer is missing some SNPs that appeared in the PLINK result fr…