Exception raise up Allele in genotype

[shichenhai2020]

INDEL ERROR: A Exception raise up when calling variant from some bam, tab txt produce success, but a blank vcf result. when move out calling deletions and insertions, vcf produce normally.

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Error Detail:
Processing: .bam
Detected reference: rcrs
Exception in thread "main" java.lang.IllegalStateException: Allele in genotype * not in the variant context [C, CCCC]
at htsjdk.variant.variantcontext.VariantContext.validateGenotypes(VariantContext.java:1359)
at htsjdk.variant.variantcontext.VariantContext.validate(VariantContext.java:1297)
at htsjdk.variant.variantcontext.VariantContext.(VariantContext.java:400)
at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:494)
at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:488)
at genepi.mut.util.VcfWriter.createVCF(VcfWriter.java:204)
at genepi.mut.pileup.PileupToolLocal.run(PileupToolLocal.java:239)
at genepi.base.Tool.start(Tool.java:193)
at genepi.base.Toolbox.start(Toolbox.java:44)
at genepi.mut.Server.main(Server.java:42)

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Parameters used:
Command [--input, *.bam, --output, *.vcf, --reference, rCRS.fasta, --level, 0.01, --deletions, --insertions]
mtDNA Low-frequency Variant Detection v1.3.0
Division of Genetic Epidemiology - Medical University of Innsbruck
(c) Sebastian Schoenherr, Hansi Weissensteiner, Lukas Forer