Subset a multisample VCF file
Based on the way you've called the command (using -xl-sn), I assume you are using GATK 4 and not GATK 3.

If this is the case, the documentation for the -xl-sn flag is available here: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_variantutils_SelectVariants.php#--exclude-sample-name.

By default, the -xl-sn SAMPLE means "exclude the sample called SAMPLE from my VCF". In your case, you're providing an entire list of samples, in a file, which is not the default behaviour. In order to tell GATK that you're providing a file and not a sample name, you need to ensure the file you provide has the extension .args.

From the documentation:


  File names must use the extension ".args"