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 aih-tih-sc-176637-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam | bcftools call -c > ./aih-tih-sc-176637-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.vcf
Generate Data Set from .
using this bed file : /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed