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?
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?