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  • #1

    GATK count covariates error - contig lengths

    Hi All,
    I have GATK error when inputing the following:

    $ java -jar GenomeAnalysisTK.jar -I /input.bam -R /hg19.fasta
    -B:dbSNP,VCF /dbsnp.b37.vcf
    -T CountCovariates -cov QualityScoreCovariates -cov ReadGroupCovar
    iate -cov CycleCovariate -cov DinucCovariate
    -recalFile /recal_data.csv


    Error: Found contigs with the same name but different lengths

    contig reads = MT / 16571
    contig reference = MT / 16569

    Is there anyway to correct the contig length issue easily for the mito DNA?
    Tags: contigs, error, gatk, length
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