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HaplotyperCaller GVCF Unkown IUB code for SNP '*'

Dear guys,

Recently, I used GATK-3.4-46 GVCF (default) to call variant from exome, all things works fine. However, when I annotated the variants with snpEff/VariantAnnotator, some error happens (fatal error read from file: )

1 6272137 rs709208 A G,* 1817.65 PASS
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '*'

Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '*'

And this error can be repeated.
While the problem does not occur in GATK-3.4-0. After checking the alteration cloumn, it seems that the <*.DEL> was replaced by *.
Does it a bug, how to fix this problem ?
PS: Could I use GATK-3.4-0 to call the variants from the exomes.

Best Answer


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