VCF file alignment to the reference genome

Question

[Sathish]

Hi everyone,

I have detected SNP and Indel for my re-sequenced reads. I have done my analysis with draft genome but now revised genome is available with chromosome wise. I have a VCF file for detected SNP and Indels information's with complete annotation. At present I would like get chromosome details of detected variations. It is possible to align my VCF files to revised genome annotation file or any alternative methods?

I'd appreciate any help on this matter.

[Ram]

Is this the human genome?

[Sathish]

It is plant genome...

Answer 1

[User 59]

So the normal way to do this would be via liftOver or a similar tool - however if you've got an updated reference you would be much better off re-aligning your reads and re-calling your variations. Working with an improved reference is likely to yield improved results in variant calling.

[Ram]

True. The RoI on liftover is not good enough to cut corners in this case.

[Sathish]

Thanks for your reply. What about CrossMap program?

[User 59]

I stand by my previous answer - it is always going to be better to remap your reads and recall your variants under almost every scenario.