Finding the coverage of variants from variant file, which has no DF4 field

Question

[a.james]

Hello All,

I have a simulated VCF file and I have simulated fastq file generated using the varsim tool. I wanna find the coverage of each variants in the vcf file. The vcf file has no filed (for example, DF4 field with coverage information). Inorder to find the coverage I first aligned the fastq files and generated BAM file. From the BAM file I have also generated mpileup file with coverages of each base. However, the pileup has no complete coverage for all variants in the vcf file. In this case, I would like to know any alternatives or options for the same

[Pierre Lindenbaum]

samtools depth with option -a ?