Discover secondary genetic predisposition in 10K cancer cases

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Folders

data

Intermediate data produced that is specific to this manuscript: 20160713_Rahman_KJ_KH_152_gene_table_list.txt: 152 curated cancer predisposition gene list (more info in Table S1 of Huang et al. Cell 2018)

PanCan_ClinicalData_V4_wAIM_filtered10389.txt: clinical data for the 10,389 passed-QC sample

all.rc_anno: readcount data of the rare variants

charged.PCA.r1.TCGAbarcode.merge.exon.ALL.vcf.samples.expanded.AFcorrected.lowAF.sele.tsv: CharGer output for the low AF variants, filtered for one version of ExAC with AF < 0.05% (control-access)

doc

Store and update the manuscript, figure, and supplementary documents.

analysis

discover_predisposition_variants/ : scripts to filter and discover the likely pathogenic and pathogenic variants

reference