Question: vcf filter dp
0
gravatar for chengyi31000
2.5 years ago by
chengyi3100010
chengyi3100010 wrote:

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 @

dp filter vcf • 1.1k views
ADD COMMENTlink modified 2.5 years ago by RamRS27k • written 2.5 years ago by chengyi3100010
0
gravatar for RamRS
2.5 years ago by
RamRS27k
Houston, TX
RamRS27k wrote:

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.

ADD COMMENTlink written 2.5 years ago by RamRS27k

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

ADD REPLYlink written 2.5 years ago by chengyi3100010
2

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.

ADD REPLYlink written 2.5 years ago by RamRS27k
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