selection of reference genome
1
0
Entering edit mode
3 months ago
Tsin-Lau • 0

hello everyone, I got a vcf file with variation called using hg38 as reference genome. I wonder what would happen if I use hg19 as reference genome to annotate these variants. Would it be OK or get wrong? Thanks!

hg19 reference genome hg38 • 532 views
ADD COMMENT
3
Entering edit mode
3 months ago

Alignment, variation-calling, and annotation should always be performed on the exact same reference. Not a similar one. If you want to use a different reference, start anew from alignment. It's also possible to use LiftOver but you'll get a different answer.

ADD COMMENT
0
Entering edit mode

Thank you for your answer! Another small question: by saying 'a different answer', do you mean the LiftOver result is not that accurate?

ADD REPLY
0
Entering edit mode

A lifted-over VCF will typically be 'mostly' the same as one generated from the target genome, especially in well-established regions of the reference that don't change much from version to version. But it's mainly useful when everything between two builds is identical except for the coordinates; when there are structural differences, or variants that span regions where a different major allele was chosen, there will be differences, and a better approach is to redo everything starting from alignment.

ADD REPLY
0
Entering edit mode

I see, thanks.

ADD REPLY

Login before adding your answer.

Traffic: 995 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6