Test-drive the GATK tools and Best Practices pipelines on Terra
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how can i get vcf file without repeat snps?
i just call snp with my several samples` RNA-seq data .
then i get several vcf files , so i just use the function "MergeVcfs" to combine them into a big vcf files.
and i use the "CollectVariantCallingMetrics" to evaluate it .
then i find that this big vcf file contain all the snps in my samples , even those snps whose share the same sites.
so what i wonder is can i get a vcf file that all snps get the unique site.
i know it may be a complicated question , because i think this kind of big vcf file contain the snps whose genotypes is different in a way.
so if i want to get a one-site-one-snp vcf file , the information about genotype may get wrong.
or my question is simplified in this way: i just want delete the repeat snps to get net number about my snps.
maybe my description is not so clear , but i am really trying my best to describe my question as best as i can.
thanks a lot.