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Dear LDSC developers,
I am trying to use LDSC to get the genetic correlation of many traits in a single sample. First, I ran --h2 to get the heritability for each trait, but often times I got nega…
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What's the effect of `--n-blocks` on the result of partitioning heritability? Using a higher `--n-blocks` can sometime solve the singular matrix error but we are not sure what side effect will that in…
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Hi,
I have a genotype data with only part of chromosome covered. I am wondering if there is way to calculate SNP-heritability based on the non-consecutive chromosomes?
Thanks,
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add support for annotation regex/globbing in the `.yml` config file.
E.g.
```yaml
HERITABILITY_INPUT:
- id: mousebrain
annotations: ["*"]
```
to run h2 analysis type on all annotations.
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Hello, thank you for the nice work. I am trying to run GENESIS on a few GWASs, and I am a bit confused with some of the parameter setting:
1) the input should includes the effective sample size, de…
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I am trying to run my own data on SUPERGNOVA,
however, I get the following error when testing:
Preparing files for analysis...
Calculating LD scores...
49351 SNPs included in our analysis...
C…
liym9 updated
6 months ago
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Hi,
I am trying to run the AnnoPred example code (when heritability estimation not provided) but got the following error. May I ask what the problem is and how can I fix it?
```
(ldsc) $ bash o…
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Hi,
I am running LDSC for genetic heritability and genetic correlation for a variety of datasets. Some of them (biobank data) have very large case/control imbalance (sample prevalence of
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How to interpret the occurrence of "NA" in the "corr" column in the result file?
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Hello, I want to analyse African GWAS data with LDSC. However, I have been unable to find LD scores with African ancestry online. I have generated LD scores using 1000G data, but I find heritability a…
xEmz updated
3 months ago