Tumor Purity for Exome Sequencing Data

[mrfox]

hi all,

I am wondering if anybody has recommendation for software tools that work well for inferring tumor purity for exome sequencing data.

Thanks a lot!

[amitm]

hi,
One way of inferring tumor purity or tumor load is check mutant allele frequency for the driver gene.
Assuming your sample is 100% pure and the driver gene mutation is a heterozygous one, then it should be around 50%.

A more informative way would be to plot the freq. of all heterozygous mut.
The median should be around 50%.


If you are using a PDX, then the above considerations get confounded (by probable mouse reads)