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Here is an interesting unexpected thing. You can find REGENIE generated extra 4 lines for chr4 (UKB imputed array), rs530960215 is the last SNPs, but I don't know why REGENIE have extra 4 line result …
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hi, thank you for your wonderful method!
i have problems when using MR-JTI to interpret my GWAS results.
problem 1:
do i need to run JTI methd before runing MR-JTI?
if not, how can i get the e…
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```
What steps will reproduce the problem?
1. Use a subversion repository on a server that is accessed via ssh using keys
2. The svn command line tool automatically will go through ssh which will
go …
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## `README.md` with commands and analyses
**2/2**
| Exercise | Points Possible | Grade |
| -------- | ------- | ------- |
| Commands for Step 1.1 | 0.33 | 0.33 |
| Commands for Step 2.1 | 0.3…
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The primary set of issues is described here: https://issues.jboss.org/browse/PLINK-666
This is a subset of the problems above:
```
2015-03-10 15:44:31,353 WARN [org.jboss.as.weld] (default task-1) J…
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I'm encountering a problem with the Michigan Imputation Server (v2.0.6). Although my VCF files pass all checkVCF.py checks without error, the imputation pipeline fails about a minute and a half into t…
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**Is your feature request related to a problem? Please describe.**
The sample data I am working with is relatively homogenous but not well characterized by any of the populations in 1000G. Additional…
dym22 updated
6 months ago
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Hello, I am using selscan to compute iHS with the 1000G 30x data.
About the 1000G 30x data I only used:
- Unrelated individuals (from CEU population)
- Phased and polarized biallelic variants
…
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Broad has release on dbGaP PCA on genotypes before imputation. Matching sample ID with self-ascertained ancestry information also found in dbGaP, I plotted PC1 vs PC2 below:
![officialpca](https://…
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Hi,
When running shapeit4 v4.1.2, I get the following error in the Initialization step:
```
Initialization:
[E::hts_hopen] Failed to open file output/1.unphased.vcf.gz.csi
[E::hts_open_format…