Extracting Snp Positions In Non-Reference Genome

Question

[GR]

Dear All,

I have access to genome assemblies of multiple individuals from the same species (eukaryote species). SNPs between the reference and non-reference have been identified and are available for public access. As per the standard format of SNP data only the position of SNP in the reference genome is given along with the bases in reference and non-reference genome. I need to know the SNP position in the non-reference genomes as well. Can someone help me what would be the best way to do this.

Many thanks, RT

Answer 1

[Pavel Senin]

In similar situation, I was extracting a sequence covering a reference SNP (say cutting at 200bp upstream and downstream) and mapping it to non-reference genome using bwa-sw - knowing where it maps, calculating non-reference SNP position is easy. parameters settings for the aligner, however, affect the quality of the process.

[GR]

Thanks a lot Pavel for this idea. I will try this if this works for me. Do you think blat will work in this case?

[Ashutosh Pandey]

BLAT should work. But I would suggest you to use short read aligner. Why See this, What should I use blat for?. I would use a 100-200 nucleotide sequence. I think that should be enough for specificity.

[GR]

Great! Thanks a lot both.

[Pavel Senin]

i didn't use blat, in my case, sam files generated by bwasw were easier to process and to interactively control the results using IGV, where you can load your non-reference genome and its annotation and to see where the SNP-containing reference sequence maps and so on.