Re-format sample columns in VCF file

Question

[phinguyen]

Hi, I'm using a tool (GLIMPSE2_concordance) requesting sample format in VCF file is GT:PL:DP. However, my vcf only has the format GT.

My VCF file	Requested VCF file

Is it possible to add format fields PL and DP to VCF, which only has the GT format field? (not re-calling variants)

I consulted the GATK4 doc, and it seems that the only way is to re-calling variants.

Does anybody have any solution to this problem? Please let me know, I am very grateful, thanks.

[barslmn]

Are the DP and PL fields on the INFO column? Maybe you can carry them to SAMPLE column from INFO. If you don't have the fields you would need to do variant calling again. GATK adds these field by default.

[phinguyen]

Unfortunately, my INFO column doesn't have DP and PL fields.

Side information: For someone who falls into a similar situation, if your INFO column has fields that need to be added to FORMAT, you could use the bcftools like this question.

[WouterDeCoster]

Does GLIMPSE2 actually use the DP and PL, or does it just expect them to be there? The difference is whether you have to figure out the right values, or could fake it.