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genepi / 23andme-tools

Convert 23andMe data to VCFs
Apache License 2.0
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Illegal base [] seen in the allele #8

Open AlanOmica opened 3 years ago

AlanOmica commented 3 years ago

Hey, I have a problem using the converter for Michigan. The terminal gives me this:

java -jar ./target/vcf-tools-0.1.jar vcf-generator --in Dani1.txt --ref human_g1k_v37.fasta --out Daniout --exclude Y,MT

Generate vcf.gz files from your 23andMe Genotype Data

java.lang.IllegalArgumentException: Illegal base [] seen in the allele at htsjdk.variant.variantcontext.Allele.create(Allele.java:231) at htsjdk.variant.variantcontext.Allele.create(Allele.java:355) at genepi.vcf.VCFBuilder.build(VCFBuilder.java:155) at genepi.vcf.VCFConverter.run(VCFConverter.java:58) at genepi.base.Tool.start(Tool.java:193) at genepi.base.Toolbox.start(Toolbox.java

Do you know where could be the problem? Thanks Erick Barlandas