How to sync vcf file with the genome?
I'm working with variants. The reference is not entire genome or chromosome but just a small region inside one chromosome. When I use bcftools to extract the VCF file from ClinVar, the returned is the variant coordinates of the region. However, if I select the fasta sequence for alignment, the coordinate of nucleotides began with the position 1. Is there any scripts or programs that sync between the extracted coordinate and the variant coordinate?
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khanhlpbao •
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