bcftools view error: "F_PASS" is not defined in the VCF header
1
0
Entering edit mode
2.6 years ago

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 • 1.3k views
ADD COMMENT
0
Entering edit mode

are you using the latest version of bcftools ?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

add functions N_PASS() and F_PASS()

ADD REPLY
2
Entering edit mode
2.6 years ago

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 COMMENT
0
Entering edit mode

Thank you! It worked.

ADD REPLY

Login before adding your answer.

Traffic: 1343 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6