as far as I understand, there is no read group with a LB attribute. https://software.broadinstitute.org/gatk/documentation/article?id=6472

Probably the input file for -l is malformatted. It must be a BED file with chr-start-end. The documentation, depending on which website you check (original VarScan page, GitHub, the VarScan2 how-to paper) is misleading at times. Given a VCF file, just do:

awk '$1 ~ /^#/ {next} {print $1, $2-1, $2}' in.vcf | sort -k1,1 -k2,2n -u > out.bed