sam morris

viridis not working after updating to ubuntu 20.04

5

Viridis was working fine on my previous version of Ubuntu 19.10. I recently updated to 20.04. When I try and use some of the viridis functions (from the R terminal),...

loftee was working fine using VEP-103. However, when I run it now using the updated VEP-107, I get the error: ``` lib/Bio/DB/BigFile.c: loadable library and perl binaries are mismatched (got...

Reccomended parameter settings for whole chromosome of genotype-density data

1

Hi, I'd like to run iSAFE on a single chromosome (6), containing ~70K individuals, 35,863 SNPs covering 170Mb. I've been trying lots of different parameter settings of different window sizes,...

What arguments should I pass to pass to run in exhaustive mode?

1

Hi @WansonChoi, Thanks for your piece of software. I'd like to run the omnibus test in exhaustive mode. However, it's not clear to me what needs passing to the --exhaustive...

Feature request: check for presence of e.g. --keep-fam file before converting to temporary psam/pvar/pgen

4

When running the command: ``` plink2 \ --bgen /well/ukbb-wtchg/v3/imputation/ukb_imp_chr${chr}_v3.bgen ref-unknown \ --sample /well/ckb/shared/ukb_dataset_210403/ukb22828_c1_b0_v3_s487276.sample \ --keep-fam ukb_eur_inds.txt \ --remove-fam not_used_in_PCs_calc_UKB.txt \ --freq \ --out ukb_imp_chr${chr}_v3.unrelated ``` returns: ``` PLINK v2.00a3.1LM AVX2...