Extract SNPs and INDELs
1
0
Entering edit mode
kredens • 0
@kredens-9281
Last seen 5.8 years ago
Brazil

Hi, I have two hsapiens genome... The first is hg38 and the second is CV. I need to extract the SNPs and INDELs comparing CV with reference to hg38. 

How I could do this?

 

Thanks for your help!!!

hsapiens snps indels • 941 views
ADD COMMENT
0
Entering edit mode
@herve-pages-1542
Last seen 7 hours ago
Seattle, WA, United States

Hi,

If you have the chainfile that describes the pairwise alignment between hg38 and CV, I think it would not be too hard to use it to extract the SNPs and INDELs. If you don't, then you need to align the 2 genomes first. I'm not aware of tools in Bioconductor that can perform this kind of alignment though. Neither pairwiseAlignment() in the Biostrings package nor msa() in the msa package will scale to the size of a Human chromosome. You'll need to look outside Bioconductor for a tool that handles this. I found this

https://www.biostars.org/p/114535/

on Biostar but it's not clear that this solution works on a big genome like Human. Maybe you'll have better luck.

Cheers,

H.

ADD COMMENT

Login before adding your answer.

Traffic: 246 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