Introduction
Tumor purity is an estimation of how much of the tumor genome sequence is different from that of the normal matched tissue as a result of mutation. A sample of only tumor cells ( containing no normal tissue ) should show a mean frequency of 0.5 for mutant alleles at heterozygous loci with somatic mutations. The contamination of tumor tissue with normal tissue, the level of which is sample-dependent, affects mutant allele frequencies and indeed decreases their relative fraction for both homozygous and heterozygous somatic mutations. We developed a novel algorithm, PurityEst (tumor purity estimation), to infer the tumor purity from the allelic differential representation of heterozygous loci with somatic mutations in a tumor sample with a matched normal tissue sample.
For help with PurityEst, please email xsu1@mdanderson.org
Downloading PurityEst
The source code and sample input files can be downloaded here.
| File | Link |
|---|---|
| PurityEst.tar.gz | download |
Running PurityEst
PurityEst takes the widely used and customized GFF files as input. Here, the GFF files for somatic mutation detection are generated by GigaBayes.