freebayes option "--region" in present in vcf file but not in log file freebayes command

[sachiwije]

Hi,

I am seeing different options for the freebayes command in the log file and the vcf

In the log file, I can see the following.

freebayes-parallel reference/ref.txt 15 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict -vcf -f reference/ref.fa SRR6346204.bam > SRR6346204.raw.vcf

But in the VCF file this command can be seen

##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa SRR6346204.bam --region CP085200:0-197289"

I'm just wondering what this refers to since I did not specify any regions.
Although the "--region CP085200:0-197289" is present in the VCF, I can see calls from positions larger than 197289.

So, I am a bit confused about what it refers to.

Snippy version is 4.6.0