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Old 11-05-2013, 06:34 AM   #1
gmarco
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Question 1000 genomes human reference

Hello,

I'm using hg19.

As you may know when you perform variant calling, reference variation allele may be biased due to the human reference we use (it's very uncommon but it does happen).

I would try a different human reference, I would like to know if there's any with 1000 genomes data. And try doing some variant callings and then compare results.

I've found the following link, but I'm not sure if this is a reference from 1000 genomes data:

ftp://ftp-trace.ncbi.nih.gov/1000gen...k_v37.fasta.gz

If someone could bring me some light on this issue.

Thank you.

Best regards.
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Old 11-05-2013, 11:53 PM   #2
gmarco
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If there's no human reference coming from 1000 genomes data, is there any other alternatives to standard hg19?
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Old 11-06-2013, 12:47 AM   #3
sophix
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Hi gmarco,

Yes, that is the reference genome if you are using the variants from phase 1.

http://www.1000genomes.org/faq/which...bly-do-you-use
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Old 11-06-2013, 02:12 AM   #4
gmarco
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Quote:
Originally Posted by sophix View Post
Hi gmarco,

Yes, that is the reference genome if you are using the variants from phase 1.

http://www.1000genomes.org/faq/which...bly-do-you-use
Then I guess 1000genomes reference for phase 2 is:

ftp://ftp.1000genomes.ebi.ac.uk/vol1...e/hs37d5.fa.gz

Maybe I miss explained myself. I want to try to map my data with a human reference based on 1000 genomes project and obviously different from hg19.

I don't know if that 1000 genomes reference available for download is the one they used in the project, or if it was generated by 1000 genomes project.

Last edited by gmarco; 11-06-2013 at 02:15 AM.
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