PLINK Error: Invalid QUAL value on line

Question

[panacotaforcota]

Dear all,

I have worked with VCF file after haplotypecaller, where QUAL=Infinity for some variants. I am trying to make PGEN format, but I have this ERROR:

Error: Invalid QUAL value on line 17 of test_123-temporary.pvar.zst.

The default range for QUAL is [0, ∞). So, I don't know why Infinity is a problem. Can you help me please with this error?

Thanks!

Answer 1

[chrchang523]

[0, 1) means 0 is included, but 1 is EXCLUDED from the interval. Similarly, [0, infinity) means infinity itself is not allowed.

[panacotaforcota]

Well, what should I do to deal with such values in QUAL when using PLINK? Maybe there are some recommendations?

[chrchang523]

I recommend writing a short script to replace all instances of QUAL=Infinity with a large value (e.g. 100) in the VCF.

(edit: in the meantime, I will modify the 12 Apr 2023 plink2 build to accept QUAL=Infinity values.)

[panacotaforcota]

Thank you a lot! It will be wonderful!