Tools to generate VCF from two FASTA, or mutant FASTA from Ref FASTA and VCF?

[jeffseq]

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

[muthu545]

Hi,

For the 2nd and 3rd questions Ref + VCF = Mut or Mut+VCF = Ref
you could use, FastaAlternateReferenceMaker tool as part of GATK package
from Broad Institute.

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_fasta_FastaAlternateReferenceMaker.html

I'm not sure you could use GATK to answer your first question... May be some others in the forum could help you with that....

--
Thanks

[jeffseq]

Thanks. Will try it out. Isn't GATK going to ask fee for it? any open source tools available?

[muthu545]

GATK is open source...