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

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  • 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.)


  • #2
    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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    • #3
      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.

      Comment


      • #4
        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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        • #5
          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 [email protected]

          It will help me a lot. Thank u so much!

          Comment


          • #6
            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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            • #7
              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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              • #8
                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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                • #9
                  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

                  Comment


                  • #10
                    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?

                    Comment


                    • #11
                      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?

                      Comment


                      • #12
                        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://[email protected]/1.2/hg19/
                        and try downloading dbsnp_132.hg19.vcf.gz <- This is what I got.

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                        • #13
                          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://[email protected]/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...

                          Comment


                          • #14
                            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.

                            Comment

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