This repository holds scripts and raw data used by the publication:
Paracchini L, Mannarino L, et al., Oncotarget (2016), in press.
and it is divided in several subdirectories:
config
: Includes configuration data for bcbio-nextgendata
: Includes results (VCFs) and other data files
The data files included are as follows:
all_genes.bed
: BED file containing all the regions used in the experimentall_somatic_variants.vcf.gz
: The complete file containing all the variants analyzedall_somatic_variants.vcf.gz.tbi
: tabix index for the above filephylogeny_table.txt
: Allelic fraction table used to generate the phylogenetic trees
Additional data files were taken from https://github.com/lbeltrame/mnegri-ov170 as they were also part of the previous publication.