Gerde / Accurity

Accurity is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome will probably work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs).

Home Page:https://www.yfish.org/display/PUB/Accurity

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Accurity

Please use Accucopy, Accurity's successor.

Accurity is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome will probably work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy, and low-coverage (as low as 1X) settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased the signal/noise gaps between different copy numbers.

Z. Luo*, X. Fan*, Y. Su, YS. Huang (2018). Accurity: Accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. Bioinformatics. https://www.ncbi.nlm.nih.gov/pubmed/29385401 https://www.yfish.org/download/attachments/327721/Luo%20et%20al%202018%20AdvanceAccess.pdf

For more information, check https://www.yfish.org/display/PUB/Accurity

To compile, go into Accurity/ and type "make debug" or "make release".

Accurity is not easy to compile. If you just want to use Accurity, please use its docker, https://www.yfish.org/display/PUB/Accurity#Accurity-Docker.

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Accurity is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome will probably work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs).

https://www.yfish.org/display/PUB/Accurity

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