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When I call Indels from my vcf file using GATK analysis tools I ger an Error!

Hi I used the GATK pipeline until I got a vcf that had SNPs and Indels, so I used GATK Analysis tools to remove SNPs and keep Indels. But after adding the reference genome, dictionary and index I get this error:

The provided VCF file is malformed at approximately line number 455: Unparsable vcf record with allele *, for input source: /home/helenadarmancier/Documents/Estagio/Original/vcf_NoAngH201_NoMono.vcf

How can I fix this?



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