Mapping two genome annotation files

Question

[Paul]

I have two reference sequences (A and B). For both A and B, I have done variant analysis and got the SNPs and Indels, respectively.

Now to annotate A and B with respect to their gene location, I have two different annotation files (for A and B, individually), though both A and B are the reference sequences from the same species.

Now my aim is to check whether the SNPs and Indels obtained using Ref sequence A, are same as the ones obtained from Ref sequence B. Since the annotation file for both the Ref sequences (A and B) are different, I am unable to map them with each other and find out the common SNPs and Indels between A and B.

Answer 1

[Pierre Lindenbaum]

lift over your VCF ? http://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf

[Paul]

will it work for Mycobacterium?

[Pierre Lindenbaum]

http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver