Download GSGP
-
VCF to GSGP
(md5: 2be4705c72a77c24082cbad0db466f5a)
The Python implementation of the GSGP algorithm. Given a VCF
file, it calculates the GSGPs for all the samples & genes &
signatures.
Contents:
-
vcf2gsgp.py: The main process of GSGP. Python>=3.8 on Linux or
MacOS system is needed. Detailed options can be obtained by
running the program with the -h parameter.
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generate_gtf.py: The Python script used to generate the gene
annotation file needed for the above program.
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model: The
COSMIC SBS mutational signatures data files.
Download Gene Annotations
The Gene Transfer Format (GTF) file used by this tool. Both the
exon and gene GTF files are required. Alternatively, users can
generate the required GTF files themselves using the
above
Python script and the GTF file(s) downloaded from the third-party
links at the bottom of this page.
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GRCh37/hg19 (Ensembl version 75)
Exon GTF
(md5: ff3599f204bc4dfe2ad35691bd498e7f)
Gene GTF
(md5: df117815244387cbf79e17e0d3e48110)
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GRCh38/hg38 (Ensembl version 99)
Exon GTF
(md5: ea99f55ac7406e1db2ffd78751847a65)
Gene GTF
(md5: 57fb157ebb9a21aa0fdaaf20c99eab53)
Third-party Links