Which types of human reference genome should be used for VCF normalization

Question

[seta]

Dear all,

I have got multiple single sample vcf files that should be merged into multi-sample vcf file. For the VCF normalization step before doing merging, could you please let me know which type of human reference genome should be used? I found here at Ensembl, but have no idea which type should be downloaded. As these vcf files resulted from whole genome sequencing and bwa aligner used for mapping step, I guess the toplevel assembly should be used, is it right? please kindly share me your suggestion and idea.

Thanks

[Pierre Lindenbaum]

why would you need some kind of different reference for merging the vcfs ?

[seta]

I didn't involved in the mapping step and have not access to the responsible person; I received just vcf files.

[Pierre Lindenbaum]

how will you merge the vcf ? a tool like "bcftools merge" doesn't need a reference while "gatk combinevariants" needs it .

[seta]

I'm going to use bcftools and as far as I know it requires reference genome for variant normalization that should be used before merging, isn't it? please let me know your idea.

[Pierre Lindenbaum]

ahh, ok , you were talking about this kind of normalization.

[Pierre Lindenbaum]

ahh, ok , you were talking about this kind of normalization.

[seta]

yeah. Could you please let me know which type of reference genome should be used in this situation? I found here from Ensembl, which type should I download?

[Pierre Lindenbaum]

you have to check in your VCF header the ##contig lines and check they are the same chromosome names and the same length than the REF