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  • How to regenerate an index file for a gzipped vcf file?

    I have a large vcf file with genomic data (330 GB) and an index file that accompanies it. I ran the command:

    bcftools view -f PASS --threads 8 -r chr9:55252802-55252810 -o output.vcf.gz -O z 722g.990.SNP.INDEL.chrAll.vcf.gz

    I get:

    [W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi
    [W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi


    I was told that I need to regenerate my index file using Tabix. I have tried the following command that seemed to work for someone else having a similar problem:

    tabix -p vcf 722g.990.SNP.INDEL.chrAll.vcf.gz

    but it returned:

    tbx_index_build failed: 722g.990.SNP.INDEL.chrAll.vcf.gz



    I am not quite sure what command I should be using to regenerate my index file. Any help is greatly appreciated!

  • #2
    This specifically ("The index file is older than the data file") is a warning and not an error. If you trust the index, you can in all honesty ignore this spammy message.
    Anyways, see if this thread helps:

    (If you want to follow that thread's suggestion, just remember that you have quite a big file to uncompress and re-compress.)
    Last edited by r.rosati; 05-28-2019, 05:34 PM.

    Comment


    • #3
      You should be able to use bcftools itself to index the file. Just use "bcftools index 722g.990.SNP.INDEL.chrAll.vcf.gz"

      Comment


      • #4
        Yes, but... if the index is just OK, he could as well do
        touch 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi
        and the message won't bother him anymore.

        Comment


        • #5
          Originally posted by r.rosati View Post
          This specifically ("The index file is older than the data file") is a warning and not an error. If you trust the index, you can in all honesty ignore this spammy message.
          Anyways, see if this thread helps:

          (If you want to follow that thread's suggestion, just remember that you have quite a big file to uncompress and re-compress.)
          Thank you so much, this seems the route I need to take!

          Comment

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