Error: Cannot compare (>) objects of dissimilar types

[yifangt]

Hello,
I was trying to filter my vcf file with:

vcffilter -f "DP > 10 & MQ > 30 & QD > 20" all_samples-raw.vcf

I always got an error and only had the header without any result:

cannot compare (>) objects of dissimilar types
3 4

Any clue to a possible fix of the problem?

[janxkoci]

I had this issue in the past, i think i solved it by using brackets like this:
... -f "( DP > 10 & MQ > 30 & QD > 20 )" ...

It also worked if i used only one annotation for filtering, that was the hint - you can try that to see if the error goes away..

[yifangt]

No, the same error stayed!

[janxkoci]

I use this filter syntax in the genotype field (-g parameter), but i would assume it works the same for -f too..

[tseemann]

I think I found the problem here.

cannot compare (>) objects of dissimilar types gets printed if one of the tags you are referring to does not exist in the VCF line.

Using the sample.vcf on github which has no NX tag:

 vcffilter -f 'DP > 10 & AF > 0.3 & NS > 2' sample.vcf # OK
 vcffilter -f 'DP > 10 & AF > 0.3 & NX > 2' sample.vcf # cannot compare (>)

[pjotrp]

I think the error message can be a little clearer