-
Hello,
I saw a few tickets reporting a similar issue when using:
./munge_sumstats.py \
--sumstats UKB.GWAS.txt \
--N 336974 \
--ignore BETA \
--out UKB_DR \
--merge-alleles w_hm3.snplist
…
-
Trying to drop the content of a single file, which will fail, because only one copy exists: `git|datalad drop `. The emphasize the performance differences, the demo uses a dataset with 250k files.
…
-
Hi @eugenegardner just wondering what the consequences of not applying any filter for the ALT/ALT genotypes would be. Very likely including false positive calls? Also do you have any idea why is this …
-
Hi,
I'm new to working with SHAPEIT.
I came across an article titled: "A General Approach for Haplotype Phasing Across the Full Spectrum of Relatedness" (2014) and would like to recreate the same f…
-
Hi @joellembatchou,
So I'm running regenie for UKB data while using the burden/skat-o options.
I was wondering if there's any workaround to include variants in which the REF allele is actually …
-
## 참고 소스/TOOL
* http://www.robots.ox.ac.uk/~vgg/data/oxbuildings/
-
Hello cTWAS developers,
Thank you for putting together this useful tool! I am in the process of implementing GWAS and had a few questions about preparing the LD matrix .RDS/ Rvar files. Specifical…
-
Hi,
I was trying to run regeneie (v2.5.3) step 2 for burden test with many genes in my gene sets for ukb exome data. It was running without any error but after a while it is throwing error:
```
…
-
For UKB ITT's synthetic data, we tested indexing each genotype as a field using its RSID as the field name. They looked like rs123, rs1234, rs12345, etc. Searching for 'rs' returns the list of genotyp…
-
Similar to #494. I already have eddy corrected data. Is there an option to only perform normalization to T1 space?
Thanks.