split-vep - cannot use arithmetic operators to compare strings and numbers

[oalavijeh]

Running bcftools v1.10 on VEP annotated file

command:
bcftools +split-vep -C Consequence -i "Consequence = 'intron_variant'" input.vcf -s primary:intron | bcftools +split +vep -c CADD_PHRED:Int -i "CADD_PHRED>=20" | bcftools +split-vep -c gnomAD_AF:Float -i "gnomAD_AF<=0.001"| bcftools view -Oz > output.vcf.gz

Error: cannot use arithmetic operators to compare stings and numbers

This works if I take out the gnomadAF_AF part. Is there a way around this error?

Many thanks

[pd3]

Can you please try with the latest version? The support for this has not been added until 1.11 I believe

[oalavijeh]

Worked thanks!

[sbaross]

I am still getting this issue when using v1.12. I am using almost identical code to that in the initial example, filtering by both CADD and gnomAD AF (however I am using -c CADD_PHRED:Float as CADD scores are not limited to integers).

I am able to filter by the CADD score numerically, but I get the error message when doing the same with the gnomAD column. I've checked on two different systems using different files and this happens reproducibly. I suspect it may be down to gnomAD AFs having scientific notation which bcftools isn't interpreting correctly while CADD scores do not?

[pd3]

@sbaross Please try first with the latest version, see here how to install from github http://samtools.github.io/bcftools/howtos/install.html or here from a tarball http://www.htslib.org/download.

If still not working, can you please open a new issue and provide a small test case to debug the problem