Question: Mapping two genome annotation files
0
gravatar for Paul
3.4 years ago by
Paul80
India
Paul80 wrote:

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.

sequencing next-gen • 817 views
ADD COMMENTlink modified 3.4 years ago by Pierre Lindenbaum130k • written 3.4 years ago by Paul80
1
gravatar for Pierre Lindenbaum
3.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

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

ADD COMMENTlink written 3.4 years ago by Pierre Lindenbaum130k

will it work for Mycobacterium?

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Paul80
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