What is the logical operator for plink2 --extract-if-info?
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Entering edit mode
3 months ago
Yiming ▴ 10

Hello,

I know this might be a stupid question, but I have tried everything I could think of. For example

plink2 --pfile input --out output --extract-if-info gnomAD_exome_ALL '<' 0.01 '&' gnomAD_exome_AFR '<' 0.01 --make-pgen
plink2 --pfile input --out output --extract-if-info gnomAD_exome_ALL '<' 0.01 '&&' gnomAD_exome_AFR '<' 0.01 --make-pgen
plink2 --pfile input --out output --extract-if-info gnomAD_exome_ALL '<' 0.01 AND gnomAD_exome_AFR '<' 0.01 --make-pgen

None of these works

Thank you very much!

plink2 • 146 views
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Entering edit mode
3 months ago

—extract-if-info only supports a single predicate at a time for now. (This isn’t actually a problem here: just split your filtering operation across two runs.)

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