Convert the NT position in a VCF file to an AA position

Question

[SaltedPork]

I have a VCF file from iVar. Looks like:

REGION  POS REF ALT REF_DP  REF_RV  REF_QUAL    ALT_DP  ALT_RV  ALT_QUAL    ALT_FREQ    TOTAL_DP    PVAL    PASS    GFF_FEATURE REF_CODON   REF_AA  ALT_CODON   ALT_AA
HXB2    712 C   T   8   0   58  5633    1034    45  0.998582    5641    0   TRUE    cds-NP_057849.4 GCG A   GTG V
HXB2    712 C   T   8   0   58  5633    1034    45  0.998582    5641    0   TRUE    cds-NP_057850.1 GCG A   GTG V
HXB2    715 G   A   5   0   41  5635    1032    46  0.999113    5640    0   TRUE    cds-NP_057849.4 CGC R   CAC H

I want to convert the second column (POS) into the amino acid position instead of nucleo tide position. I have a GFF file for the genome, are there any programs that can do this?

[Pierre Lindenbaum]

this has been asked many times. Search this site for snpeff, vep, etc...