vgteam
Variant IDs in the vcf file
Hi, I have two fastq files. I map them to a same graph and then genotype them use vg call in the same parameters. So I get two vcf files. I want to know if the third column (the variant id) in the vcf file is share between the two vcf files? I mean , if there are same ids in the two files , are they same variants? Thank you!
They are the same site, and the reference allele [0] would be consistent. But the alt alleles could be different. Ex you could have something like A->AA,AT in one and A->AA,AG in the other (so allele 2 is AT in one file and AG in the other).
If you run calling with vg call -a then put the results through bcftools merge I think you shuold get a consistent file.
