GSGP

Step 1: select VCF file
VCF or gzip-compressed VCF with GT (genotype),
AD (allelic depths), and DP (read depth) fields is needed.
Multi-sample VCF is also supported. File size should be smaller than 10Mb.
Step 2: select genome
Step 3: advanced parameters
Min read depth
The minimum value of read depth (DP field in VCF).
(limit: ≥0)
Min VAF
The minimum value of variant allele frequency (VAF).
(limit: 0-1)
Max VAF
The maximum value of variant allele frequency (VAF).
(limit: Min VAF - 1)
Presets
Max upstream distance
The maximum base pairs that allows the variant to be located upstream of the gene.
(limit: 0-300kb)
Max downstream distance
The maximum base pairs that allows the variant to be located downstream of the gene.
(limit: 0-300kb)
Exon variant weight
The weight of exon variants when a variant can be annotated to multi-genes.
(limit: ≥0)
Intron variant weight
The weight of intron variants when a variant can be annotated to multi-genes.
(limit: ≥0)
Upstream variant weight
The weight of upstream variants when a variant can be annotated to multi-genes.
(limit: ≥0)
Downstream variant weight
The weight of downstream variants when a variant can be annotated to multi-genes.
(limit: ≥0)

citation: Ji X, Wang E, Cui Q. Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. Brief Bioinform. 2023;bbad017. PMID: 36682004