jonicoleman / gwas_scripts Goto Github PK

do we have gene-based analysis script? thanks.

Thanks for your paper and the code. I'm learning to QC the chip data and I am confused by the filtering steps in script: Iterative_Missingness.sh
You iteratively remove the SNPs and samples by a sequential threshold (0.1, 0.09, 0.08, ..., 0.01 when the arguments are set as 90 99 1) with this script while my previous understanding of filtering by missing rate is to remove SNPs and samples by one rate (say 0.05 or 0.1). What is the point of doing the consequent filtering and how is that better than just remove by a single threshold? Wouldn't this be too stringent in general?
Looking forward to your response. Thanks in advance!

Hi Joni,
Any plan to add "Hail" module?
Thanks
Shicheng

Hi,

I am attempting to do some QC, but when I get to the code for doing the sex check and I run:

plink
--bfile $root.LD_two
--split-x b38
--make-bed
--out $root.LD_split

I get the error:

Warning: 1918 het. haploid genotypes present (see
/users/k1469373/brc_scratch/pelotas/from_hamel/final_zcall/Brazil_Pelotas_GSAMDv2_intensity_data_zcall_final.LD_split.hh); many commands treat these as missing.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands treat these as missing.
Total genotyping rate is 0.999403.
285784 variants and 997 people pass filters and QC.
Among remaining phenotypes, 694 are cases and 286 are controls. (17 phenotypes are missing.)
Error: --split-x cannot be used when the dataset already contains an XY region.

Sorry, I am very new to Plink and I'm a bit worried if I try to fix this willy-nilly on my own I will mess something up without realizing it! If you have any advice it would be much appreciated.

Thanks!
Jess