query for samtools

Question

[viswanathrana29]

Hi all, I have .vcf file of nelumbo nucifera genome and i have also display the variants with the help of tview commands in samtools for nelumbo nucifera genome. then how can functional annotate the variants which are displayed? any software are available for this, help me for this thank you

Answer 1

[Pierre Lindenbaum]

there is a gff file available for nelumbo nucifera at : ftp://ftp.ncbi.nih.gov/genomes/Nelumbo_nucifera/GFF/ , then follow Best way to annotate a VCF file with a GFF File