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Hi
I have been using SAIGE-GENE+ (specifically the GBAT test) extensively for the past couple of months. I now want to run the GBAT analysis with my own groupFiles. I am generating these groupFiles…
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"Expects LD scores formated as required by the original LD score regression software. Weights for the european population can be obtained by downloading the eur_w_ld_chr folder in the link below (Note…
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Dear Developing Team
Great thanks for this beautiful package and all the efforts in harmonising the GWAS summary data as well integrating the MR methods.
I have recently noticed there are some …
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I'm having a problem running coordinate genotypes (between UKbb ref panel + sumstats + validation_genotypes).
Example run command:
```
ldpred coord --gf UKBB20_CEU_REF.merged.hm3_only \
…
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Current:
```
1. for each table
2. create `docs_by_id` generator
3. call `bulk()` with `docs_by_id` generator. This will index 500 documents at a time
```
Say there are 1000 participants and …
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I found that postgap --summary_stats skips some variants from summary statistics file (variants that are parsed with --rsID and passes the threshold) and there are defferent number of variants in post…
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Hi everyone,
I'm using mvSuSiE to do fine-mapping for two highly correlated traits (rg=0.6, estimated by LDSC) in UKBB at one 1Mb region.
Before running mvSuSiE , I performed the single-trait fi…
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iv been getting this error when running fastBAT and iv tried everything that i can think of to fix it but this very uninformative error message is bewildering to me as i cant think of a reason why…
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Is it possible to work with a different genome species? Can I incorporate an alternative annotation file for plotting?
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This is a great work! I want to know whether you can provide the LD information of between SVs/STRs and SNPs? or provide all SVs/STRs/SNPs at the individual level?