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Error using SelectVariants

NourNour GermanyMember
edited May 2016 in Ask the GATK team

I constantly get this error ERROR MESSAGE: Input filesmgp.v3.indels.rsIDdbSNPv137.vcf and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.

ERROR /mgp.v3.indels.rsIDdbSNPv137.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X]
ERROR reference contigs = [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2, 3, 4, 5, 6, 7, 8, 9, MT, X, Y, JH584295.1, JH584292.1, GL456368.1, GL456396.1, GL456359.1, GL456382.1, GL456392.1, GL456394.1, GL456390.1, GL456387.1, GL456381.1, GL456370.1, GL456372.1, GL456389.1, GL456378.1, GL456360.1, GL456385.1, GL456383.1, GL456213.1, GL456239.1, GL456367.1, GL456366.1, GL456393.1, GL456216.1, GL456379.1, JH584304.1, GL456212.1, JH584302.1, JH584303.1, GL456210.1, GL456219.1, JH584300.1, JH584298.1, JH584294.1, GL456354.1, JH584296.1, JH584297.1, GL456221.1, JH584293.1, GL456350.1, GL456211.1, JH584301.1, GL456233.1, JH584299.1]

However, the file mentioned in the error (the one with less contigs) is actually downloaded from the Sanger institute website and according to their description it's based on the same mouse genome reference GRCm38. (available here: ftp://ftp-mouse.sanger.ac.uk/REL-1303-SNPs_Indels-GRCm38).
I really am looking forward to your answer!
Thanks in advance!
P.S. changing the header didn't help ... and using SortVcf gave the following error:
"Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52.0" ....


  • SheilaSheila Broad InstituteMember, Broadie admin
    edited May 2016


    I just had a look at the VCF header, and it seems like the contigs are all sorted like the reference, however, the MT and alternate contigs are not present. Perhaps in the VCF index file, the order is not the same? In any case, are you using Java 1.8? Picard requires Java 1.8. Also, can you please post the exact command you are running for SortVcf?


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