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RealignerTargetCreator parameter -known [File] fails when creating .idx file.

CoryzaCoryza EnschedePosts: 11Member

Hi,

I'm trying to use the RealignerTargetCreator as a test with 1 know file; 1000G_phase1.indels.b37.vcf. At first the contigs didn't match with my .BAM file (chr1/chr2 vs 1/2), so I adjusted that. Now when running it for the first time; java - jar [path to genomeAnalysisTK.jar] -T RealignerTargetCreator -R [.fasta] -I [.bam] -o [.intervals] -known [path to 1000g_phase1_adjusted.indels.b37.vcf] it gives the following error: "I/O error loading or writing tribble index file for [path to 1000g]". When running it the second time, I get the following error; "Problem detecting index type", because the .idx file is not correctly created.

What am I doing wrong?

Best Answer

Answers

  • CoryzaCoryza EnschedePosts: 11Member
    edited April 23

    Also when formatting the data file from chr1/chr2 to 1/2 and don't change the indel files, I get the same error. EDIT: When downloading the .idx files instead of creating them, it works. How can this happen?

    Post edited by Coryza on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,869Administrator, GATK Developer admin

    Do you mean you used scripting tools to modify the contig names in your resource files? If so that's the wrong thing to do, because there may be more differences between the reference builds than just the contig names. You should always download the resource files that match the correct version of the reference, not convert them yourself, because that is unsafe. The index issue is just one symptom of that.

    Geraldine Van der Auwera, PhD

  • CoryzaCoryza EnschedePosts: 11Member

    I've done as you suggested. Downloaded both the genome (ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.8/hg19) and 2 indel files, named above. Keep having the same problem (there are .idx files also to download, but I wonder why RealignerTargetCreator won't do that).

    `##### ERROR MESSAGE: I/O error loading or writing tribble index file for G:\Stage_Enschede\methods_GenomeAnalysisTK\GenomeAnalysisTK-3.1-1\indels\1000G_phase1.indels.hg19.vcf

    ERROR --------------------------------------------------------------------

    ----------------------`

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