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

Searched on Google with the first line of a JAVA stack trace?

We can recommend more relevant solutions and speed up debugging when you paste your entire stack trace with the exception message. Try a sample exception.

Recommended solutions based on your search

Samebug tips

Do you know how to solve this issue? Write a tip to help other users and build your expert profile.

Solutions on the web

via GitHub by mmokrejs
, 9 months ago
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0
via GitHub by jrobinso
, 9 months ago
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0
via GitHub by mmokrejs
, 9 months ago
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3793131: unparsable vcf record with allele 0
java.lang.RuntimeException: 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 org.broad.igv.tools.IgvTools.createTribbleIndex(IgvTools.java:1062)
at org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:981)

Users with the same issue

You are the first who have seen this exception. Write a tip to help other users and build your expert profile.

Write tip

Know the solutions? Share your knowledge to help other developers to debug faster.