first question: i have a vcf file resulted from samtools, belonging to a mammalian that assembled in scoffold level. I annotated it and now want to extract non-synonymous SNPs and found genes containing ns SNPs. how i can extract sequences of genes that have ns SNPs to blast them and finding gene names.
second question is: how can i extract indels that located in genic region (in annotated vcf file) and get its length to plot it?
thanks in advance