How to get SNV abundance in NGS analysis

Question

[biock]

After SNV calling, I need to find each SNV's abundance, which means the variant's proportion in all reads that contain the position. How to get the value, and what tools I need to use?

Answer 1

[ATpoint]

After variant calling, you should have a VCF file. VCFs contain a DP field both in their INFO and FORMAT columns, indicating total and ALT depth. There is good documentation about VCFs out there. Spend some quality time reading it.