Getting truncated PVAR file when converting BGEN file

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Thon de Boer

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Aug 18, 2020, 8:38:33 PM8/18/20
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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

This is the command line I used
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...

Any ideas?

Thon

Christopher Chang

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Mar 15, 2021, 11:16:17 AM3/15/21
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For the record, this was resolved in plink2-users: https://groups.google.com/g/plink2-users/c/v_ScFwBLOSc/m/Z6MYYViuBgAJ .
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