Read Depth in varFilt -D

[eric.fuchs]

Hello all,

I'm new to bioinformatics and I'm trying to teach myself most of these things.

I just called snp's with samtools and mpileup. I then proceeded to filter using:

bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf

I'm a bit confused on why I should worry about filtering on *maximum* read depth rather than on minimum. Shouldn't I select a minimum read depth and allow for the maximum to go as high as possible? Could this lead to other sorts of trouble?

Thanks for help or redirecting me to the proper source,

Eric,

[adaigle]

I know this post is several months old and you've hopefully figured it out by now, but I have a similar question I'm hoping someone else will stop by.

Here is the answer to your question I found in a helpful mpileup tutorial (link): “We don’t want to trust SNPs at sites with super high coverage, because they might be represent variation between variable copy number repeats, i.e., the reads that map to this location in the reference are actually from duplicated sites in your sample; you can–and should–change this parameter based on the kind of coverage you have in your dataset, e.g., -D500.”

What I'm wondering is how exactly you figure out what number to use? Is there any rule of thumb for what to do with your coverage information to know how many reads are too many?

Hope you figured your stuff out