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Error using SelectVariants
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" ....