how to combine contigs into chromosomes in vcf file

Question

[Chenfei Zheng]

Dear all,

A long time ago, I resequenced about 100 individuals and called variants mapping against an older version of the reference genome which contained 500 contigs.

However, the latest version of the reference genome was updated into chromosome level and it only contained 8 chromosomes.

So is there any solution for assembling the contigs into the latest chromosomes in my vcf file without recalling variants again?

Thank you

[GenoMax]

Since the genome likely changed significantly between the two versions re-aligning and then calling the variants is probably the best way to go.

[Chenfei Zheng]

Thank you for help.