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Hkins552 07-05-2011 07:16 AM

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?

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