Hello, I have short read data from multiple samples stored as scaffolds.vcf.gz files. I have some gene sequence of interest. I want to find the closest homologous sequence of the respective genes from all the other samples. At first, I thought it would be easily doable by creating a Blast database, but as these are short read data and not assembled whole genome sequences, I cannot do a BLAST search.

Can you please give me any suggestions on how can I extract the homologous sequences of a gene from multiple .vcf.gz files? Thank you.