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to combine multi-sample variants with tumor-normal comparison vcf files.

caileicailei ShanghaiMember

Dear all,

When I combined multi-sample variants with tumor-normal comparison vcf files, following errors emerged. It is normal for triallelic variants in tumor. Could you please tell me how to fix the error? Thanks a lot.

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: The provided VCF file is malformed at approximately line number 2457: unparsable vcf record with allele A/C
ERROR ------------------------------------------------------------------------------------------


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