I am having a problem merging all chromosomal UK biobank files. I ran the following command.
plink2 \ --bfile /path/to/file/ukb_imp_chr1 \ --pmerge-list /path/to/file/merge.list \ --maf 0.01 \ --hwe 1e-6 \ --make-pgen \ --out /path/to/file/ukb_imp_allchr
I also tried
plink2 \ --bfile /path/to/file/ukb_imp_chr1 \ --pmerge-list /path/to/file/merge.list \ --maf 0.01 \ --hwe 1e-6 \ --make-bed \ --out /path/to/file/ukb_imp_allchr
The merge.list has the following content from chromosome 2 onwards.
/path/to/file/ukb_imp_chr2 /path/to/file/ukb_imp_chr3 /path/to/file/ukb_imp_chr4 ... /path/to/file/ukb_imp_chr22 /path/to/file/ukb_imp_chr23 /path/to/file/ukb_imp_chr24
However, once I run the command, I do not get a merged .bed file. I only get a .psam file with the following result:
Using up to 24 threads (change this with --threads). --pmerge-list: 24 filesets specified (including main fileset). --pmerge-list: 487409 samples and 1 phenotype present. --pmerge-list: Merged .psam written to /path/to/file/ukb_imp_allchr-merge.psam .
Is there something wrong with the command?
In both instances
--make-bed, I only get the psam file but nothing else.
Also is there any possibility to export to bgen/pgen to reduce file size as all individual chromosomal .bed files are at lest 200-920GB in size.