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  • GATK: VCF file for Local realignment around indels

    Hello,

    I'd like to perform a 'Local realignment around indels' on bam file uisng GATK. However I'm still unclear about the vcf file with the known indels that I should provide. I'd say that the 'dbsnp_132.hg19.vcf' file included in the bundle should do as it seems to include indel data. Also, should I filter out non-indels form that file in order to speed up the realignment?

    I'd be grate if someone could comment on this.

    Thanks
    Jorge

  • #2
    Probably all the files you will need are avaiable at :

    ftp://ftp.broadinstitute.org/bundle/1.2/hg19/

    For indels you should use the file: ftp://[email protected]

    Inserted with the command: -B:indels,vcf 1000G_biallelic.indels.hg19.vcf

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    • #3
      Thanks a lot for the information!

      Jorge

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