PyVCF assigns a QUAL value of '.' instead of zero

[knewl]

Hello,

This is an issue in PyVCF where instead of a zero a '.' is written to the QUAL field of a VCF. The issue was raised a few years ago and is therefore unlikely to be addressed soon.

For example, this variant with QUAL of 0.0 in sample_name.1.vcf

MN908947.3 7576 . T TA 0.0 PASS DP=2.0;DPS=0.0,2.0 GT:GQ 1:0

has a QUAL value of '.' once it is merged into sample_name.merged.vcf

MN908947.3 7576 . T TA . PASS DP=2.0;DPS=0.0,2.0;Pool=1 GT:GQ 1:0

This causes an error in vcf_filter.py when it attempts to assess whether the quality is < 20:

TypeError: '<' not supported between instances of 'NoneType' and 'int'

My suggestion would be to ignore variants in vcf_filter.py where v.QUAL is not numeric.