Shiny App for visualising whole genome sequencing QC metrics of tumour samples
Includes:
- Sample summaries
- QC metric plots
Plot descriptions:
- AT DROPOUT: AT sequence dropout rate
- GC DROPOUT: GC sequence dropout rate
- UNEVENNESS: Unevenness of coverage, calculated as local coverage RSMD
- MAPPING RATE: Percentage of mapped reads
- CHIMERIC READS: Percentage of chimeric reads
- DEAMINATION: Percentage of deamination mutations (C:G to T:A)
- GENOME COVERAGE: Median whole genome coverage
- COSMIC COVERAGE: Percentage of COSMIC Cancer Genes at <30X coverage
- FRAGMENT SIZE: Average library fragment size in bp
- MUTATIONAL BURDEN: Log number of SNVs and Indels
- DUPLICATION: Percentage of PCR duplicates
Sample types:
- FF = "Fresh frozen" tumour tissue
- FFPE = "Formalin-fixed paraffin embeded" tumour tissue
Test data includes a small set of annonymised samples.
Dummy input data table available here:
https://github.com/martimij/CancerQC_v2/blob/master/QC_dummy_table.csv