To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

BaseRecalibrator - Input files knownSites and reference have incompatible contigs

I am trying to use GATK BaseRecalibrator but I get this error:
"Input files knownSites and reference have incompatible contigs"

" ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs. Please see more information. Error details: The contig order in knownSites and reference is not the same; to fix this please see: (, which describes reordering contigs in BAM and VCF files..

ERROR knownSites contigs = [chr1, chr10, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr11, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, ......
ERROR reference contigs = [chr1, chr10, chr11, chr11_KI270721v1_random, chr12, chr13, chr14, chr14_GL000009v2_random, chr14_GL000225v1_random, chr14_KI270722v1_random, chr14_GL000194v1_random, .....

I searched the Internet and found out that I should use the compatible vcf file and reference, but I downloaded vcf file from hg38 bundle so I suppose it should be compatible. My reference uses 'chr1,etc.', while the vcf file uses '1,2,etc.', so I added chr to the vcf file. I also used Picard ReorderSam on my BAM file and SortVcf on vcf file as described here
Now it looks like my reference is sorted differently (lexicographically sorted). I have no idea how can I fix this problem, should I sort my reference or download other reference file?


Sign In or Register to comment.