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error concerning vcf file with dbSNP in base recalibration

SophiaSophia Member
edited November 2016 in Ask the GATK team

I am running BaseRecalibrator in GATK 3.6 for mouse mm10, using dbSNP 142 for mm10, and am getting this error:

"The provided VCF file is malformed at approximately line number 11959: VCF support for complex rearrangements with breakends has not yet been implemented"

The line it refers to seems to be a line like any other line (taking line 11959 without counting the header lines):

1 8458354 rs257549955 A G . . RSPOS=8458354;GENEINFO=71096:Sntg1;dbSNPBuildID=137;SAO=0;VC=snp;VP=050000080001000000000100

May this error have something to do with the compression of the vcf file (it is bgzipped and tabix-indexed)?

I also tried with a recent nightly build, GenomeAnalysisTK_nightly-2016-11-08-g9f0580f.jar, which returned the same error.

Any ideas to fix this will be welcome!


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