gistic_reference

Code adapted from gistic2 github repo and snputil repo

Designed to update last GISTIC reference (Gencode v22) to Gencode v36 but code adaptable to create any GISTIC reference given appropriate inputs

Steps and Output:

Input: GTF for reference file (can be downloaded from https://www.gencodegenes.org/human/releases.html)

Steps:

1. Parse GTF using scripts/20240228_gencode_xtrct.R (adapt paths as needed) --> save TSV
2. Import TSV into scripts/create_rg_file.mlx (adapt paths as needed)

Output: New reference Matlab object for GISTIC use

Additional Files:

CNV Blacklist:

• data/hg38_GDC_SNP6_CNV_list.161107.txt : original GISTIC CNV blacklist from SNP6 array analysis
• data/filtered_hg38_SNP6_GDC_CNV_blacklist.txt : new GISTIC CNV blacklist derived from removing overlaps between above file and Cancer Gene Census (as of 03/08/2024)

To-Do: create updated blacklist from WGS panel analysis