I am upgrading samtools/bcftools from 1.3.1 to 1.5 and I am trying to 
understand a difference I spotted.

Using bcftools 1.3.1:

> samtools mpileup -uf ref.fna sample.bam | ./bcftools-1.3.1/bcftools call -c 
> --ploidy 1 - 

gyrA    284     .       A       G       77.0075 .       
    GT:PL   0:107,127

Using bcftools 1.5:

> samtools mpileup -uf ref.fna sample.bam | bcftools call -c --ploidy 1 -

gyrA    284     .       A       .       49.9963 .       
       GT:PL   0:107

in both cases samtools was version 1.5

I just wondered what has changed in bcftools for it to call the variant in 
version 1.3.1 but not in 1.5 ? By the way, the change must have happened 
between 1.3.1 and 1.4 as 1.4 gives the same result as 1.5 above)

Looking at the release notes for 1.4, is this related to "Improved calculation 
of the QUAL score particularly for REF sites"? 

Thanks for any help


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