I am converting the UKBB GEN formatted file for use in PLINK2 to PGEN format, but I am consistently getting truncated files that seem to end in the middle of a line...
bluebee@bbench:~/ukbb/genotypes$ tail chr21.pvar
21 48043815 rs77375664 T G
21 48043904 rs537966753 A G
21 48043934 rs111552696 A G
21 48043992 rs7282606 G A
21 48043996 rs535732839 C T
21 48044005 rs142435765 C T
21 48044020 rs768987899 C T
21 48044021 rs571687629 G A
21 48044043 rs545365966 C T
21 48044047 rs9984956 bluebee@bbench:~/ukbb/genotypes$ wc chr21.pvar
1259002 6295013 35520512 chr21.pvar
plink2 --bgen ukb_imp_chr21_v3.bgen ref-first --sample ukb57143_imp_chr21_v3_s487296.sample --out chr21
I tried the latest release as well as stable alphe 2.3...