Question: How to get SNV abundance in NGS analysis
0
gravatar for biock
2.1 years ago by
biock50
biock50 wrote:

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?

snp ngs gatk • 675 views
ADD COMMENTlink written 2.1 years ago by biock50
3
gravatar for ATpoint
2.1 years ago by
ATpoint36k
Germany
ATpoint36k wrote:

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by ATpoint36k
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