bcftools expression string exact match
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Entering edit mode
11 months ago
roalva1 ▴ 80

Hello, If I execute this in bcftools 1.10.2

clinvar.vcf.gz is https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz

bcftools query -i "CLNREVSTAT='criteria_provided,_conflicting_interpretations'"  -f '%CLNREVSTAT\n' clinvar.vcf.gz | sort -u
I get this results:
criteria_provided,_conflicting_interpretations
criteria_provided,_multiple_submitters,_no_conflicts
criteria_provided,_single_submitter

I was expecting to get only criteria_provided,_conflicting_interpretations. Is there anything that I don't understand.

Many thanks

bcftools • 230 views
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Entering edit mode
11 months ago

I supect it's invoked as an OR operator. Can you please try

"CLNREVSTAT='criteria_provided' &&  CLNREVSTAT='_conflicting_interpretations' "
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Entering edit mode

Yes it seems so,

also I execute this:

 bcftools query -i "CLNSIG='Pathogenic'"  -f '%CLNSIG\n' clinvar.vcf.gz | sort -u
The result is
Pathogenic
Pathogenic,_Affects
Pathogenic,_association
Pathogenic,_association,_protective
Pathogenic,_drug_response
Pathogenic,_drug_response,_other
Pathogenic,_other
Pathogenic,_protective
Pathogenic,_risk_factor

I think it is applying the OR also to the results. This is not my desire behavior :(

Thanks for the answer

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