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  • Error GATK - Generating interval file

    Hello,

    To generate interval file usign GATK is needed a .bed file to specify the positions of human exome (hg19) (let's say "all_captured_exomes.bed").

    To get this file, I went to UCSC and specify certain parameters to get this .bed file. So, concretely :


    And when I try to launch the aligner :

    java -jar $GATK_HOME/GenomeAnalysisTK.jar -T RealignerTargetCreator \
    -R /home/armand/mnt/cubix/Genomes/index/index/hg19/bwa_path/Homo_sapiens_assembly19.fasta \
    -I $1 -log intervals.log -B:dbsnp,vcf $dbSNP \
    -L ../exome_hg19_captured/all_captured_exomes.bed -o "$core_dir/${core_name}.intervals"


    It gives me this error :
    ##### ERROR MESSAGE: File associated with name ../ref_gen_hg19/exome_hg19_captured/all_captured_exomes.bed is malformed: Interval file could not be parsed in either format. caused by Invalid command line: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary
    Any ideas what could it be?

    Thanks for your time!,

  • #2
    Hi, you need to have the contig/chromosome IDs in the reference.fasta EXACTLY as in the VCF or BED file, and properly sorted. Also any other scaffolds/contigs in the ref.fasta not in the VCF or BED or vice-versa will cause errors. My solution was to remove all scaffolds/contigs not found in the VCF I used from my ref.fasta which has worked (so far!). Good luck!

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