Question: How to get SNV abundance in NGS analysis
0
gravatar for biock
15 months ago by
biock10
biock10 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 • 508 views
ADD COMMENTlink written 15 months ago by biock10
3
gravatar for ATpoint
15 months ago by
ATpoint24k
Germany
ATpoint24k 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 15 months ago • written 15 months ago by ATpoint24k
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