GATK genotypemergeoption Error

Question

[bioinformatics98]

Hi all,

I am trying to run a single sample dataset of a paired-end sample obtained for exome sequencing (Read 1 and Read 2) through the seqmule pipeline and it gives this error:

NOTICE: normalzing VCF with Vt...
NOTICE: done normalzing.
NOTICE: keep variants if they are unfiltered in any one of the input files.
NOTICE: extracting variants shared by at least 2 input files.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef): 
##### ERROR
##### 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
##### 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
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Duplicate sample names were discovered but no genotypemergeoption was supplied. To combine samples without merging, specify --genotypemergeoption UNIQUIFY. Merging duplicate samples without specified priority is unsupported, but can be achieved by specifying --genotypemergeoption UNSORTED.
##### ERROR ------------------------------------------------------------------------------------------
Failed to merge VCF files
NOTICE: Cleaning...

When I looked at "genotypemergeoption" everywhere (in all the files and directories), they all had UNSORTED provided in the command for "genotypemergeoption", so I do not understand why the error is telling me that "genotypemergeoption" was not supplied.

Any help will be very much appreciated! Thank you!