gravatar for gary.napier

2 hours ago by

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: 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

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modified 1 hour ago

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2 hours ago
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gary.napier0



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