Help with extracting information from browser

[Andrew Cassidy]

Hi all,

Can anyone provide guidance on how to extract a list of SNPs with high minor allele frequency (MAF ~0.25–0.5) in Malaysian/Southeast Asian populations please?

I eventually want to group these into phased macrohaplotyes.

Kindest Regards

—————
Dr Andrew Cassidy
Independent NGS Technology and Genomics Consultant
Blue Yonder Genomic Insights
Email: ajca...@blueyonder.co.uk

https://www.linkedin.com/in/ajcassidy/
https://www.researchgate.net/profile/Andrew-Cassidy-4

Strategic Genomics with a Personal Approach

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

The following paper argues that the 1000 Genomes project doesn't include enough Malaysian sequences and sequenced 100 more healthy individuals with an average of 30-fold coverage. The data appears to be in dbVar:

https://www.ncbi.nlm.nih.gov/dbvar/studies/estd201/

You can download the VCF file from the paper and then filter for your MAF cutoff.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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[Andrew Cassidy]

Dear Jairo,

Thank you very much for the response and excellent background information.

In light of this additional data I have reached out to the Singapore team for their up to date data sets on the local population of Malays.

However, for completeness, I would like to extract the same information from genome browser data and do a comparison. You have already been very helpful but some guidance on how to do this would be much appreciated.

Thank you again.

Kindest Regards
—————
Dr Andrew Cassidy
Independent NGS Technology and Genomics Consultant
Blue Yonder Genomic Insights
Email: ajca...@blueyonder.co.uk

https://www.linkedin.com/in/ajcassidy/
https://www.researchgate.net/profile/Andrew-Cassidy-4

Strategic Genomics with a Personal Approach