superFreq | Analysis pipeline for cancer sequencing data | Genomics library

superFreq is a R library typically used in Artificial Intelligence, Genomics applications. superFreq has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

You need the aligned bam files of the exomes, and a preliminary (liberal) variant calling through for example varScan, mutect, multiSNV or any other similar software. superFreq is not sensitive to false positives in these VCFs. The details of this doesn't affect output much as long as all the somatic and germline variants are present. In house we typically use samtools and varscan:. From version 1.3.0, superFreq will automatically run this command in case the .vcf files linked in the meta data are missing. Note that this requires both samtools and varscan to be available in the system environment in which the superFreq R session is running. SuperFreq also requires a set of (at least 2, 5+ is better) reference normal samples from the same sequencing technology and exome capture. Preferably sequenced in the same lab. These samples do not have to be related to the analysed cancer exomes.