Genomic locations of the SNPs in the vaf file

[ImNotaGit]

Hi, thanks for developing this very useful tool.

When using fastq files as input, SNPs in the resulting vaf files are listed with only sequential indices (1, 2, 3, etc.), and it appears that the order of these SNPs is different from that in the bed file. Is there a way to map the SNPs in the vaf file back to their genomic locations? I would need this information because I would like to visualize the vaf data along the chromosomes for QC purposes. Thanks for your help in advance.