bcftools view error: "F_PASS" is not defined in the VCF header

Question

[Luther_Blisset]

When I run this command:

bcftools view -i 'F_PASS(GT!="mis")>0.9' <file.vcf.gz>

I get this error:

Error: the tag "F_PASS" is not defined in the VCF header

My command seems to follow the syntax in the example on this page: http://samtools.github.io/bcftools/bcftools.html where it is stated as F_PASS(GQ>90 & GT!="mis") > 0.9.

The only difference I can see is that I have removed the GQ>90 & part, which still makes sense syntactically.

Why would bcftools view mistake a (boolean) command for a file header?

Thanks

[Pierre Lindenbaum]

are you using the latest version of bcftools ?

[Luther_Blisset]

Hi, I am using bcftools 1.7 (Using htslib 1.7-2).

[Luther_Blisset]

I am using bcftools 1.7 (Using htslib 1.7-2).

[Pierre Lindenbaum]

version 1.9: https://github.com/samtools/bcftools/releases/tag/1.9

add functions N_PASS() and F_PASS()

Answer 1

[Pierre Lindenbaum]

update bctools and try again...

F_PASS was added in version 1.9: https://github.com/samtools/bcftools/releases/tag/1.9

add functions N_PASS() and F_PASS()

[Luther_Blisset]

Thank you! It worked.