Highly Variable SNP

Question

[Sebastian]

Hello,

How do we detect highly variable/ Highly polymorphic SNP's in genome. Say I need to find the a set of highly variable SNP from each chromosome of human genome.

Is there any tool or database to find this. Hope to hear from you

Answer 1

[natasha.sernova]

Look here, it may be helpful:

http://www.humgen.nl/SNP_databases.html

But this article from 2012 is also good:

Human Genome Sequencing in Health and Disease

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656720/

Answer 2

[rkostadi]

Data from the 1k human genomes has ALT allele frequencies. I would download it from: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html And, then select biallelic SNPs with high frequency of ALT allele (columns 6-10).

Answer 3

[Sebastian]

Thank you It worked.

[WouterDeCoster]

Please used ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow. In addition, if answer were useful it's appropriate to up vote those answers. If your question is resolved, mark the answer as accepted.

Answer 4

[Sebastian]

I need to retrieve a set of SNP from each chromosome (exon region )human where each SNP's have a gap of 100000 bp. the snp's should be evenly distributed. The frequency is also needed for this

Please suggest any web tools /methods