Which types of human reference genome should be used for VCF normalization
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
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why would you need some kind of different reference for merging the vcfs ?
I didn't involved in the mapping step and have not access to the responsible person; I received just vcf files.
how will you merge the vcf ? a tool like "bcftools merge" doesn't need a reference while "gatk combinevariants" needs it .
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.
ahh, ok , you were talking about this kind of normalization.
ahh, ok , you were talking about this kind of normalization.
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?
you have to check in your VCF header the
##contiglines and check they are the same chromosome names and the same length than the REF