When possible, results are made available on Github. However, some results are either too large to host or contain potentially identifiable information and cannot be made publicly available.
To run the scripts in this directory, the user must populate the following directories with large data files with specific naming conventions.
Simple chrX genotyping uses a matrix of ref/alt supporting reads from GATK HaplotypeCaller.
SCAN2 v0.9 produces R data files (.rda) in snv/[sample_ID]/somatic_genotypes.rda and indel/[sample_ID]/somatic_genotypes.pon_filter.rda. These files must be made deposited in scan2_somatic_genotype_rdas/{sSNVs,sIndels}/[sample_ID].rda.