I have whole genomic sequencing data (variant call were obtained in VCF files)for four siblings. Among the four sequenced siblings, three were affected by some kind of cancer and one was normal until now.
I wonder if there exists any bioconductor/R pakcakes or other tools where appropriate statistical test was implemented to find associated or related variation to this cancer? Now, we have only the genotype information for the four siblings without parent genotypes.
Any suggestions for further or deeper analyses for the genotype data of this four siblings? Many thanks!