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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). 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. PDF

ensembl-vep

The Variant Effect Predictor predicts the functional effects of genomic variants

gatk

Official code repository for GATK versions 4 and up

hla-polysolver

Fork of the Polysolver project

htslib

C library for high-throughput sequencing data formats

pvactools

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

vep_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)