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  • GATK: sorting vcf file given a reference file

    Hello,

    I'm using GATK to call SNPs but and my reference fasta file and vcf are not in the same order.

    is there a canned script that allows you sort the vcf file according to a given reference sequence?

    Thanks
    Jorge

  • #2
    Originally posted by jorge View Post
    Hello,

    I'm using GATK to call SNPs but and my reference fasta file and vcf are not in the same order.

    is there a canned script that allows you sort the vcf file according to a given reference sequence?

    Thanks
    Jorge
    Buen dia Jorge, tengo un regalo para usted:

    here you can find my script to sort a VCF by a reference genome. You'll need a *.dict file, which you can generate with Picard.

    enjoy!

    Comment


    • #3
      Hello,

      Thanks a lot!

      Jorge

      Comment


      • #4
        Originally posted by NGSfan View Post
        Buen dia Jorge, tengo un regalo para usted:

        here you can find my script to sort a VCF by a reference genome. You'll need a *.dict file, which you can generate with Picard.

        enjoy!

        http://code.google.com/p/vcfsorter/
        very useful, thanks.

        Comment


        • #5
          thank you!

          Comment

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