How to find de novo mutation in trio sequencing data in perl or python script?

Question

[897598644]

I only know de novo mutations(DNMs) definition as follows:De novo mutation: An alteration in a gene that is present for the first time in one family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents or in the fertilized egg itself. Gene review (http://www.ncbi.nlm.nih.gov/books/NBK5191/ )

But how to write scripts to find it?

I will appreciate if you give all possilble instances and outline of scripts!

Thnx in advance~

Answer 1

[Vivek]

The initial step is to phase your variant calls. There are existing tools to do this.

• GATK - PhaseByTransmission
• Beagle
• denovogear
• DNMFilter

Once you've phased your variant call set, you can always write a simple script to identify loci that violate mendelian inheritance patterns within the offspring and validate them.

[897598644]

Glad to see your post.

As with GATK-PhaseByTransmission,there was a link which spoke ill of this software. What is more, it seems that tools of denovogear and DNMFilter are not common used by researchers, especially in journals of nature and nature genetics,etc.

I was wondering:

1. how your engineer finishes this task
2. if it would be difficult to find DNMs by scripts from the beginning.

Hoping for your reply.

[Vivek]

Not sure how you think that link speaks ill of PhaseByTransmission when the poster specifically acknowledged making a mistake in his interpretation there.

Denovogear is based on a nature publication.

http://www.nature.com/ng/journal/v43/n7/full/ng.862.html

If you want to write a script by your own, you could look at the approach suggested in the following paper

http://www.nature.com/nature/journal/v488/n7412/full/nature11396.html

[897598644]

http://www.nature.com/nature/journal/v488/n7412/full/nature11396.html

Excuse me: the link above showed the filter argument, but did not specify what to extract from the vcf file and how to tell the DNMs from others.I have script skills but can not have expert knowledge in heredity.

I would appreciate if you gave me some detailed examples.

Thx in advance!