Set the path to your reference file with the NCM_REF environment variable
eg. export NCM_REF=/<path>/<to>/<reference>

1.14
samtools mpileup -uf $NCM_REF -l /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam | bcftools call -c > ./1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.vcf
Generate Data Set from .
using this bed file : /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed