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 -uI 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
I supect it's invoked as an OR operator. Can you please try
"CLNREVSTAT='criteria_provided' && CLNREVSTAT='_conflicting_interpretations' "
Yes it seems so,
also I execute this:
bcftools query -i "CLNSIG='Pathogenic'" -f '%CLNSIG\n' clinvar.vcf.gz | sort -uThe 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
see the "Notes" section here https://samtools.github.io/bcftools/bcftools.html#expressions
Comma in strings is interpreted as a separator and when multiple values are compared, the OR logic is used.
Seems like this applies to both the value used in the expression and to the contents of the field you are querying.
In one of my cases, I wanted to filter on an INFO tag like TAG=val1,val3,val4 (a field with comma-separated string values), and include variants with certain values but exclude variants with other values. Since you cannot use both -i and -e simultaneously I ended up just | piping the output of the first into the second one ; bcfools filter -i 'TAG="val1,val2"' input.vcf | bcftools filter -e 'TAG="val3,val4"'
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