Hello everyone,
I have snpeff output (.vcf and html). from that I want to extract below information with their co-ordinate (detail information)
Nonsynonymous (missense, nonsene)
I know their numeric values (missense and nonsense mutation) from html file but I want detaile information
Note: I have below information
synonymous_variant 130673
splice_region_variant&intron_variant 9440
upstream_gene_variant 1248890
intron_variant 343467
downstream_gene_variant 1198401
3_prime_UTR_variant 41314
missense_variant 189835
5_prime_UTR_premature_start_codon_gain_variant 3257
splice_region_variant&synonymous_variant 1321
start_lost 619
5_prime_UTR_variant 22475
missense_variant&splice_region_variant 2083
intergenic_region 1351028
splice_acceptor_variant&intron_variant 1164
stop_gained 7423
stop_lost&splice_region_variant 929
splice_donor_variant&intron_variant 1066
splice_region_variant&stop_retained_variant 136
stop_lost 1094
stop_gained&splice_region_variant 134
splice_region_variant 14560
stop_retained_variant 197
initiator_codon_variant 29
start_lost&splice_region_variant 1
But I dont know which category falls under Nonsynonymous (missense, nonsense).
Can anyone please tell me how to get detailed information of Nonsynonymous from snpeff output.
Thank you Inadvance