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How to generate a database SNP with non-model species?
Foer generating a vcf file contain multiple samples, It seems that I need a database SNP or variants
I want to generate vcf file containing multiple samples of birds for analyzing population genomic data with plink,
so I think I can use UnifiedGenotyper to generate the vcf.
From the tooldocs of UG, I know that I may need a database.vcf files to let GATK know how many substitution site in birds genome, but there's no known site of SNPs or INDELs of my research system before.
I already have 40 birds' variants which have been done recalibration two times.
So, can I generate the know site from my samples' vcf files for calling variants containing multiple samples ?