Hi,
I am doing QC to the UK biobank imputed genotype data (in pgen format) using PLINK2. One of the QC criteria is --hard-call-threshold .05. There is no indication in the .log file on the number of variants removed because of this criterion, although it has been registered as "an option in effect" by PLINK2. Please see below for an elaboration of the issue.
Here is what the .log file looks like:
Options in effect:
--geno 0.1
--hard-call-threshold .05
--hwe 1e-15
--mach-r2-filter 0.8 2
--make-bed
--memory 20000
--mind 0.1
--out ../geno/dat/v1/imputed-chr1-v1
--pfile ../geno/dat/v0/imputed-sel-chr1-v0
--threads 3
Start time: Thu Apr 13 14:25:38 2023
Random number seed: 1681388738
1018721 MiB RAM detected; reserving 20000 MiB for main workspace.
Using up to 3 compute threads.
337394 samples (181188 females, 156206 males; 337394 founders) loaded from
../geno/dat/v0/imputed-sel-chr1-v0.psam.
25906 variants loaded from ../geno/dat/v0/imputed-sel-chr1-v0.pvar.
Note: No phenotype data present.
Calculating sample missingness rates... done.
0 samples removed due to missing genotype data (--mind).
337394 samples (181188 females, 156206 males; 337394 founders) remaining after
main filters.
Calculating allele frequencies... done.
--geno: 96 variants removed due to missing genotype data.
--hwe: 5 variants removed due to Hardy-Weinberg exact test (founders only).
--mach-r2-filter: 20428 variants removed.
5377 variants remaining after main filters.
Writing ../geno/dat/v1/imputed-chr1-v1.fam ... done.
Writing ../geno/dat/v1/imputed-chr1-v1.bim ... done.
Writing ../geno/dat/v1/imputed-chr1-v1.bed ... done.
Note for each of the QC criteria other than --hard-call-threshold , i.e., --geno, --hwe, and --mach-r2-filter, PLINK2 provides the number of variants removed. Given a total of 25906 variants from the input file, after taking out these variants, 5377 variants remain. So --hard-call-threshold 0.05 did not remove any variants.
I wonder why this option did not do anything in my case and any ways to fix the issue?
Thanks in advance.
