java.lang.RuntimeException

htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0

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Stack trace

  • java.lang.RuntimeException: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0 at org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:998) at org.broad.igv.tools.IgvTools.run(IgvTools.java:393) at org.broad.igv.tools.IgvTools.main(IgvTools.java:259) Caused by: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0 at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:539) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43) at org.broad.igv.feature.tribble.VCFWrapperCodec.decodeLoc(VCFWrapperCodec.java:58) at org.broad.igv.feature.tribble.VCFWrapperCodec.decodeLoc(VCFWrapperCodec.java:43) at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502) at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:464) at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338) at htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:223) at org.broad.igv.tools.IgvTools.createTribbleIndex(IgvTools.java:1062) at org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:981)

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