Question: What tool should I use to identify the ancestry (e.g EUR or TSI or CEU) of a single human using genotyped VCF file?
1
gravatar for shajib.sust
3.9 years ago by
shajib.sust40
United States
shajib.sust40 wrote:

Hi,

I have genotyped a single person from Platinum Genome dataset of Illumina. I want to identify the ancestry of this person (NAXXXXXX) using his/her genotyped VCF file and population panel data (e.g. EUR or TSI or CEU) from hapmap. What tool should I use to do that? Any literature explaining the method to do it will also be very helpful for me. Please suggest...

With Kind Regards,

-Ruhul

 

latest clustering ancestry hapmap • 1.6k views
ADD COMMENTlink modified 3.9 years ago by Philipp Bayer6.5k • written 3.9 years ago by shajib.sust40
2
gravatar for Philipp Bayer
3.9 years ago by
Philipp Bayer6.5k
Australia/Perth/UWA
Philipp Bayer6.5k wrote:

I'd download the HapMap data from PLINK, merge that with your vcf data using PLINK2 --merge, then run any population stratification program on that and see where your single data point clusters -

I can recommend fastSTRUCTURE since that one uses PLINK's bed as input, or EIGENSTRAT which gives you a nice PCA plot but is a bit harder to run.

Alternatively, you could just get a list of ancestry-related SNPs ("Ancestry Informative Markers", like here: http://www.nature.com/ejhg/journal/v22/n10/full/ejhg20141a.html ) and manually compare your SNPs, that's easier but a bit more messy.

ADD COMMENTlink written 3.9 years ago by Philipp Bayer6.5k
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