Look at the following three files (simplified), from any two we should be able to generate the third one. Are there any tools can do the work? i.e. by compare Reference file 1 and Mutant file 2 to generate VCF file? or from Reference file 1 and VCF file to generate Mutant file 2? or from Mutant file 2 + VCF file to generate file 1?
1. Ref FASTA file
>Reference
AAATTTAGAA
2. Mutant FASTA file
>Mutant
ACATTAGCCAT
3. VCF file (partial)
POS REF ALT
2 A C
5 TT T
8 G GCC
10 A T
1. Ref FASTA file
>Reference
AAATTTAGAA
2. Mutant FASTA file
>Mutant
ACATTAGCCAT
3. VCF file (partial)
POS REF ALT
2 A C
5 TT T
8 G GCC
10 A T
Comment