Closed monagai closed 10 months ago
The entire expression needs to be quoted, otherwise what the program is passed to by the shell is FILTER~multiallelic
rather than FILTER~"multiallelic"
. So the correct command is
bcftools filter --exclude 'FILTER~"multiallelic"'
More recent versions give an error message which is hopefully more informative:
Could not parse the expression, an unquoted string value perhaps? FILTER~multiallelic
Hi @pd3 I really thank you quick and proper reply. It works.
I'm really sorry for my lack of attention. Though I had tried "FILTER~multiallelic", I hadn't thought of it.
Thank you!
No worries. It's an easy mistake to make, shell expansions are sometimes tricky
bcftools 1.13 Using htslib 1.13
bcftools filter --exclude FILTER~"multiallelic" xxx.vcf
causesNo such INFO field: multiallelic
Why does this command cause error? Why
INFO
field??? Of course, there aremultiallelic
s in the FILTER field in xxx.vcf. bcftools view causes the same error.