Using the Ensembl's Variant Effect Predictor (VEP) program I evaluated the variants identified form GATK::MuTect2. The output looks like this:
Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra
. 1:15710417 A ENSMUSG00000092083 ENSMUST00000170146 Transcript synonymous_variant 1512 1512 504 S tcC/tcA - IMPACT=LOW;STRAND=1
. 1:15710417 A ENSMUSG00000092083 ENSMUST00000175681 Transcript synonymous_variant 1832 1512 504 S tcC/tcA - IMPACT=LOW;STRAND=1
rs32076694 1:15833428 G ENSMUSG00000025925 ENSMUST00000027057 Transcript synonymous_variant 863 849 283 L ttA/ttG - IMPACT=LOW;STRAND=1
rs32076694 1:15833428 G ENSMUSG00000025925 ENSMUST00000188371 Transcript synonymous_variant 968 936 312 L ttA/ttG - IMPACT=LOW;STRAND=1
Here I picked four rows with two without SNP annotation (start with two dots) and two with SNP annotation (rs32076694, rs32076694). As you can see there are columns for 'protein position' (504, 504, 283, 312) and 'Amino_acids' (S, S, L, L). My question is whether there is an existing program that can help me retrieve a longer protein motif such like 10 amino acids centered on the mutated ones.