Off topic:bcftools view filter exclude not working when using logical operators
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4.2 years ago
curious ▴ 750

I am trying to filter a vcf to exclude variants where the INFO values R2<0.9 AND MAF<0.1 with bcftools 1.9

This appears to filter R2 correctly:

bcftools view -e 'R2<0.9' my_fav.vcf.gz

This appears to filter MAF correctly:

bcftools view -e 'MAF<0.1' my_fav.vcf.gz

This still seems to include some variants where MAF or R2 do not satisfy my conditions:

bcftools view -e 'MAF<0.1 & R2<0.9' my_fav.vcf.gz

Actually this looks like it might be giving me results with MAF<0.1 OR R2<0.9

How do I filter MAF AND R2?

vcf bcftools bcf • 1.2k views
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