Thank you! It worked.
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Luther_Blisset •
bcftools view error: "F_PASS" is not defined in the VCF header
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
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1 answer
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()
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Pierre Lindenbaum
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are you using the latest version of bcftools ?
Hi, I am using bcftools 1.7 (Using htslib 1.7-2).
I am using bcftools 1.7 (Using htslib 1.7-2).
version 1.9: https://github.com/samtools/bcftools/releases/tag/1.9