Filtration to detect de novo SNVs in trio data

Question

[Shin Taguchi]

Hi all.

I seek information about de novo SNVs created during one generation from trio data. The software used was varscan.

The result was a vcf file output containing 1478777 SNVs, which I believe contains many false positives because there are too many loci. What would be the appropriate filtering to extract truly de novo SNVs from this?

First, following the official varscan manual, I am planning to extract loci with a depth of 20 or more.

I would appreciate any other ideas or advice you might have.

Thank you.

[Pierre Lindenbaum]

The software used was varscan.

is it WGS ? use a modern CNV caller like manta or delly

[Shin Taguchi]

Yes, it is WGS.

Are those software better than varscan?

Answer 1

[colindaven]

Maybe you've seen this blogpost from brentp, it might be helpful.

https://brentp.github.io/post/variant-filter/

He's written some tools for this kind of analysis as well.

[Shin Taguchi]

colindaven

Thank you for your advice! I will check this URL.