How can I keep INFO value when convert bgen to VCF by using plink2?
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5 weeks ago
MHSATO • 0

I am working on file handling for GWAS. When I converted bgen to VCF by using plink2 with a commands below, all INFO (and also FILTER) columns became "." in the output VCF files. A column named IMP which correspond to imputed or not was disappear.

plink2 --bgen ref-first file.bgen --sample file.sample --keep id_list.txt --export vcf-4.2 bgz --out out

How can I keep INFO and some other informative columns when I convert bgen to VCF by using plink2?

Thanks,

VCF plink2 GWAS bgen • 271 views
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5 weeks ago

bgen files don't contain INFO/FILTER columns.

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Thanks so much. I miss understood about the data structure of bgen.

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