ccbc/snpitty repository overview

Exploration and visualization of next-generation sequencing data originating from targeted multi-gene panels is crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions-of-interest coupled with dynamic heuristic filtering of genetic aberrations is however lacking.

Therefore, we developed the web-application SNPitty which allows interactive visualization and interrogation of Variant Call Format (VCF) files by utilizing B-allele frequencies and coverage metrics.

SNPitty is best applicable to display variant alleles and allelic imbalances with a focus on loss of heterozygosity (LOH) and copy number variation using genome-wide heterozygous markers and somatic mutations. Moreover, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets-of-interest.

Due to dependencies on the latest R and BioConductor versions, it is highly advised to use this pre-compiled Docker image which contains an out-of-the-box working SNPitty and all features.

Source code and additional information: https://bitbucket.org/ccbc/snpitty⁠

Dockerfile used to generate Docker: https://bitbucket.org/ccbc/snpitty/src/master/docker/Dockerfile⁠