Convert missing single dot to "./."?

[bbimber]

Hello,

The single dot can indicate a missing genotype; however, some tools like beagle do not parse this correctly. Is there a way to convert these? I was hoping setGT would do this, but I am not having any luck. Should this or something like it work?

bcftools +setGT $VCF -o test.vcf -- -t '.' -n './.'

[pd3]

This is now possible with

bcftools +setGT test.vcf -- -t . -n c:./.

[bbimber]

thank you!

[Sreelekshmi-291]

Hi,
I tried the above command to convert the "." to "./.", but the single dot remains.
bcftools +setGT sample.vcf.gz -- -t . -n c:./. | bcftools view -Oz -o sample.modified.vcf.gz

Please notice the highlighted part.

Is there any other way to do this?

Thank you

[Sreelekshmi-291]

I have been using an older version of bcftools, updating it to the latest version solved the issue for me.
Thanks