tHapMix: simulating tumour samples through haplotype mixtures

tHapMix: simulating tumour samples through haplotype mixtures

MOTIVATION Large-scale rearrangements and copy number changes combined with different modes of clonal evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable variant calling tools and create well-calibrated benchmarks. RESULTS We developed a new simulation framework tHapMix that enables the creation of tumour samples with different ploidy, pu...

Tumour Simulating Spina Bifida

The patient enjoyed excellent health from his childhood up to the age of 21, when he felt a peculiar sensation of heat and burning over his waist. On rubbing his finger over the part, he felt the skin a little raised. The pain and the swelling lasted for a fortnight or so when it was cured by a hakim of his place. Three months after the alleged cure, he noticed a fluctuating tumour about the si...

Simulating haplotype blocks in the human genome

SUMMARY A bioinformatic tool was written to simulate haplotypes and SNPs under a modified coalescent with recombination. The most important feature of this program is that it allows for the specification of non-homogeneous recombination rates, which results in the formation of the so-called 'haplotype blocks' of the human genome. The program also implements different mutation models and flexibl...

Ectopic Kidney Simulating Ovarian Tumour

Benign pleural lesions simulating tumour.

Without the aid of thoracotomy it is often difficult to establish a diagnosis in cases of tumour in the thorax. Certain forms of benign pleural changes are likely to be misinterpreted as intrapulmonary, and operation for suspected lung tumour may be carried out. In the cases described here, it was possible to establish the diagnosis without employing thoracotomy. As very little attention appear...