phasing de novo mutations

[krawitz]

Hi folks,

Let's suppose I called the variants in a parent child trio and filtered for de novo mutations in the child. I am now interested in the phase, that is, I would like to know whether the mutation originated in the male or female germ line. Under certain circumstances this is possible: I there is a read covering not only the de novo site but also a heterozygous polymorphism that can only have been transmitted from one parent, this information can be used for phasing.

Let's have a look at the following pseudo vcf file:

#chr pos child father mother
chr1 10 0/1 0/0 0/0
chr1 20 0/1 0/1 0/0

The second line can be phased without any further knowledge:
chr1 20 1|0 0/1 0|0

Now, if the first heterozygous mutation is on the same read as the second, then we know also the phase of this variant:
chr1 10 1|0 0|0 0|0
chr1 20 1|0 0/1 0|0

Vice versa, if the first heterozygous mutation and the second one are not on the same read, the de novo mutation arose in the maternal germ line:
chr1 10 0|1 0|0 0|0
chr1 20 1|0 0/1 0|0

Does anyone know about a software tool that does this kind of phasing?

Thanks a lot!

peter