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Old 09-21-2015, 03:10 PM   #1
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Default GATK Base Quality Recalibration error

Hi! I tried to run GATK base recalibrator and ran into a problem. My command was "java -jar /path/to/GenomeAnalysisTK.jar -T BaseRecalibrator -I sample1_vs_hg38_realigned.bam -R hg38.fa -knownSites testing_1.vcf -o sample1_vs_hg38_recal_data.grp".

The error I got is:
ERROR MESSAGE: Input files /path/to/testing_1.vcf and reference have incompatible contigs: No overlapping contigs found.
##### ERROR /path/to/testing_1.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY]

I'm new to variant calling analysis and not sure why there is no overlapping contigs found.

unknown_0912 is offline   Reply With Quote
Old 09-21-2015, 05:12 PM   #2
Location: Guangzhou China

Join Date: Aug 2013
Posts: 82

You have inconsistent chromosome names - 1,2,3... for your input vcf file and chr1,chr2,chr3... for your reference genome file.
An edit on either file should fix the problem.
yueluo is offline   Reply With Quote

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