How Add data in ref column in vcf file

Question

[misbahabas]

Asslamu Alikum

I have vcf file look like

chr2 104 . T <non_ref> . . . T:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,45

chr2 105 . T <non_ref> . . . GT:AD:DP:GQ:PL 0/0:1,1:2:0:0,0,0

chr2 104 . T <non_ref> . . . T:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,45

chr2 105 . T <non_ref>. . . GT:AD:DP:GQ:PL 0/0:1,1:2:0:0,0,0

Is it possible to add nucleotide in ref column?

Answer 1

[aays]

It is, but it would require providing a fasta file of the reference when initially calling the VCF from a bam file in GATK.

I'm not sure what was used to make your VCF file, but I'm going to hazard a guess that it was HaplotypeCaller, in which case the relevant documentation can be found here (with the reference fasta file fed to the -R argument).