I've extracted the distinct mutations from a set of VCF files:

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SAMPLE
chr1    66480    .    AT    A    205    .    (...)
chr1    626686    .    CCT    C    124    .    (...)

and generated the predictions using SnpEff:

(...)
1    66481    *    -T    DEL    Hom    205    0        OR4F5.1    OR4F5    mRNA    NM_001005484            UPSTREAM: 2610 bases            
1    626687    *    -CT    DEL    Hom    124    0        OR4F29.1    OR4F29    mRNA    NM_001005221.2            UPSTREAM: 4652 bases        
1    626687    *    -CT    DEL    Hom    124    0        OR4F16.1    OR4F16    mRNA    NM_001005277.2            UPSTREAM: 4652 bases

now I'd like to join those results with my VCFs. But, as you can see, SnpEff change the way the alternate bases are defined. Do you know any way to join those files ?

Thanks.

EDIT:

here is my temporary C++ solution: it converts the VCF to SnpEff:

    (...)
    while(getline(in,line,'\n'))
     {
     if(line.empty()) continue;
     if(line[0]=='#')
         {
         cout << "#Chromo\tPosition\tReference\tChange\t" << line << endl;
         continue;
         }
     tokenizer.split(line,tokens);
     string chrom=tokens[0];
     if(chrom.compare(0,3,"chr")==0) chrom=chrom.substr(3);
     int pos;
     numeric_cast<int>(tokens[1].c_str(),&pos);
     string ref=tokens[3];
     string alt=tokens[4];
     if(ref.size()<alt.size()) /* AC/A = DELETION */
         {
         assert(ref[0]==alt[0]);
         ref.assign("*");
         alt[0]='+';
         ++pos;
         }
     else if(ref.size()>alt.size())
         {
         assert(ref[0]==alt[0]);
         alt.assign(ref);
         alt[0]='-';
         ref.assign("*");
         ++pos;
         }
     else
         {
         //single SNP
         }
     cout     << chrom
        << "\t"<< pos
        << "\t" << ref
        << "\t" << alt
        << "\t" << line
        << endl;
     } (...)