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Old 11-01-2011, 01:35 AM   #1
alexbmp
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Default Does anybody know how to convert dbsnp to .vcf (variant calling format)?

The title implies my core question.

Does anybody know how to convert dbsnp to .vcf (variant calling format)?

I've downloaded dbsnp from UCSC annotation site,

but I wonder if there is any tool to convert dbSNP info to vcf format.

Or should I by code change dbsnp to vcf?

(Thinking of the time wasted for searching the program I think I might have coded this thing already... or maybe not...

but if there is any utility to convert dbsnp format to vcf then there seems to be no need to do so.)

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Old 11-01-2011, 05:49 AM   #2
Bukowski
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Or just download dbSNP in VCF format from the NCBI:

ftp://ftp.ncbi.nlm.nih.gov/snp/organ...9606/VCF/v4.0/
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Old 11-01-2011, 02:27 PM   #3
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Quote:
Originally Posted by Bukowski View Post
Or just download dbSNP in VCF format from the NCBI:

ftp://ftp.ncbi.nlm.nih.gov/snp/organ...9606/VCF/v4.0/
Thank you for your reply.

The thing is, I have to get an older version (dbSNP of hg18 like dbSNP130),
but I don't think it's on the web.
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Old 11-01-2011, 02:43 PM   #4
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I have an imperfect Perl script to do this for dbSNP128 for the mouse. I say "imperfect" as it only handles simple SNPs (I could ignore complex variants such as multiallelic SNPs and indels for my purposes). I'm happy to email it to you if you are interested.
Pete
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Old 11-01-2011, 04:21 PM   #5
alexbmp
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Quote:
Originally Posted by PeteH View Post
I have an imperfect Perl script to do this for dbSNP128 for the mouse. I say "imperfect" as it only handles simple SNPs (I could ignore complex variants such as multiallelic SNPs and indels for my purposes). I'm happy to email it to you if you are interested.
Pete
Wow! Really?

It'll be so nice! My e.mail is alex2bmp@gmail.com

It will help me a lot. Thank u so much!
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Old 11-02-2011, 03:42 AM   #6
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Quote:
Originally Posted by alexbmp View Post
Thank you for your reply.

The thing is, I have to get an older version (dbSNP of hg18 like dbSNP130),
but I don't think it's on the web.
I'm pretty sure that the VCF file has information on which release any given snp was introduced to dbSNP, so you could filter for variants appearing in releases up to and including 130, and then use a liftOver tool to convert the vcf to hg18.

Not saying this is a better way than scripting it, just that there's more than one way to skin a cat
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Old 11-02-2011, 01:38 PM   #7
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Quote:
Originally Posted by Bukowski View Post
I'm pretty sure that the VCF file has information on which release any given snp was introduced to dbSNP, so you could filter for variants appearing in releases up to and including 130, and then use a liftOver tool to convert the vcf to hg18.

Not saying this is a better way than scripting it, just that there's more than one way to skin a cat
That's an excellent way to skin this particular cat.
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Old 02-10-2012, 10:18 AM   #8
jfb
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I too want to download a dbSNP file in vcf format from UCSC so I can also use their filtering tools. Isn't VCF the preferred format for dbSNP? I'm new to this field so maybe I'm missing something, but am I wrong to be surprised that such a simple thing is not available from UCSC? I guess I'll get it from NCBI and then filter it in a 2nd step.
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Old 02-10-2012, 04:04 PM   #9
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Thanks all. Actually I have downloaded dbSNP in vcf from another site.
I still have not found any tool to convert flat dbSNP to VCF.
By the way, this liftOver tool Bukowski mentioned seems to be a really nice one!
Thanks everybody
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Old 02-10-2012, 07:42 PM   #10
adaptivegenome
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Quote:
Originally Posted by Bukowski View Post
Or just download dbSNP in VCF format from the NCBI:

ftp://ftp.ncbi.nlm.nih.gov/snp/organ...9606/VCF/v4.0/
Is this where you can get dbSNP VCF for hg19?
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Old 02-10-2012, 07:43 PM   #11
adaptivegenome
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Quote:
Originally Posted by alexbmp View Post
Thanks all. Actually I have downloaded dbSNP in vcf from another site.
I still have not found any tool to convert flat dbSNP to VCF.
By the way, this liftOver tool Bukowski mentioned seems to be a really nice one!
Thanks everybody
What site?
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Old 02-10-2012, 11:58 PM   #12
alexbmp
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Quote:
Originally Posted by genericforms View Post
What site?
Sorry for this late reply.
Actually I didn't download NCBI dbsnp in VCF format;
I got it from the Broad Institute ftp ad dbsnp_132.hg19 in VCF format.

go to wget ftp://gsapubftp-anonymous@ftp.broadi...ndle/1.2/hg19/
and try downloading dbsnp_132.hg19.vcf.gz <- This is what I got.
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Old 02-11-2012, 04:22 AM   #13
adaptivegenome
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Quote:
Originally Posted by alexbmp View Post
Sorry for this late reply.
Actually I didn't download NCBI dbsnp in VCF format;
I got it from the Broad Institute ftp ad dbsnp_132.hg19 in VCF format.

go to wget ftp://gsapubftp-anonymous@ftp.broadi...ndle/1.2/hg19/
and try downloading dbsnp_132.hg19.vcf.gz <- This is what I got.
I appreciate it. I was looking for a dbSNP set for hg19...
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Old 04-05-2015, 10:24 PM   #14
zhangyong
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Quote:
Originally Posted by alexbmp View Post
Thank you for your reply.

The thing is, I have to get an older version (dbSNP of hg18 like dbSNP130),
but I don't think it's on the web.
I am wondering where did you find dbSNP of hg18, especially dbSNP132. could you give me the link to it? Thank you very much.
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