Question: bcftools view error: "F_PASS" is not defined in the VCF header
0
gravatar for gary.napier
3 months ago by
gary.napier20
gary.napier20 wrote:

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

bcftools • 88 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by gary.napier20

are you using the latest version of bcftools ?

ADD REPLYlink written 3 months ago by Pierre Lindenbaum128k

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

ADD REPLYlink written 3 months ago by gary.napier20

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

ADD REPLYlink written 3 months ago by gary.napier20

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

add functions N_PASS() and F_PASS()

ADD REPLYlink modified 3 months ago • written 3 months ago by Pierre Lindenbaum128k
2
gravatar for Pierre Lindenbaum
3 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

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()

ADD COMMENTlink modified 3 months ago • written 3 months ago by Pierre Lindenbaum128k

Thank you! It worked.

ADD REPLYlink written 3 months ago by gary.napier20
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