VCF rare variants and exon

Question

[raalsuwaidi]

Dear all,

i am new to the new genomics field. i have a vcf file which i managed to extract. i need your help filtering it to identify rare variants and exonic and non-exonic loci. i couldnt find much options in bcftools though.

thanks in advance

[gab]

Try to annotate it for example in VEP (https://grch37.ensembl.org/info/docs/tools/vep/index.html) and than you can easily filter coding variants from the apposite column it gives to you

[raalsuwaidi]

Thank you so much. I will give it a try