vcf filter dp

Question

[chengyi31000]

I want to filter Dp to my vcf file using VCFtools.

vcftools  --vcf myfile.vcf  --min-meanDP 5 --recode --out filter_DP

I want to know how to determind the number of DP for filter?

Some using Dp>5

Some using Dp>10

Thank you @

Answer 1

[Ram]

10 is a good number unless your sequencing is not really high quality. That said, Your Mileage May Vary. Start off with the more stringent filter here, and as long as you record all the filters you use as you go downstream, you should be fine.

[chengyi31000]

But when I using DP>5 my snps filter from 222414883 to 5208804. Is it right?

[Ram]

There is no right or wrong here. You need to understand your data and your task at hand better if you'd like to figure out if you're moving in the right direction. I cannot help you with that, as I am not familiar with either of those.