Important notice
As iCAGES depends on modules to call web API of DGIdb, please make sure that your PC/Mac is connected to the Internet. Thanks!
ANNOVAR input
For beginners, the easiest way to use iCAGES is to annotate somatic mutations in ANNOVAR input format with reference genome version hg19. This exemplary input file is provided in iCAGES package.
[cocodong@biocluster ~/]$ head input.txt
1 12919840 12919840 T C
1 35332717 35332717 C A
1 55148456 55148456 G T
1 70504789 70504789 C T
1 167059520 167059520 A T
1 182496864 182496864 A T
1 197073351 197073351 C T
1 216373211 216373211 G T
10 37490170 37490170 G A
10 56089432 56089432 A C
[cocodong@biocluster ~/]$ icages.pl input.txt
VCF input with one sample with his/her somatic mutations only
If you have somatic mutations for one sample in VCF file format with reference genome version hg19, iCAGES can automaticaly detect the input format and analyze your data. This exemplary input file is also provided in iCAGES package.
[cocodong@biocluster ~/]$ cat input.vcf
##fileformat=VCFv4.1
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621,assembly=b37>
##contig=<ID=2,length=243199373,assembly=b37>
##contig=<ID=3,length=198022430,assembly=b37>
##contig=<ID=4,length=191154276,assembly=b37>
##contig=<ID=5,length=180915260,assembly=b37>
##contig=<ID=6,length=171115067,assembly=b37>
##contig=<ID=7,length=159138663,assembly=b37>
##contig=<ID=8,length=146364022,assembly=b37>
##contig=<ID=9,length=141213431,assembly=b37>
##contig=<ID=10,length=135534747,assembly=b37>
##contig=<ID=11,length=135006516,assembly=b37>
##contig=<ID=12,length=133851895,assembly=b37>
##contig=<ID=13,length=115169878,assembly=b37>
##contig=<ID=14,length=107349540,assembly=b37>
##contig=<ID=15,length=102531392,assembly=b37>
##contig=<ID=16,length=90354753,assembly=b37>
##contig=<ID=17,length=81195210,assembly=b37>
##contig=<ID=18,length=78077248,assembly=b37>
##contig=<ID=19,length=59128983,assembly=b37>
##contig=<ID=20,length=63025520,assembly=b37>
##contig=<ID=21,length=48129895,assembly=b37>
##contig=<ID=22,length=51304566,assembly=b37>
##contig=<ID=X,length=155270560,assembly=b37>
##contig=<ID=Y,length=59373566,assembly=b37>
##contig=<ID=MT,length=16569,assembly=b37>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor
1 12919840 . T C . . . GT 1|1
1 35332717 . C A . . . GT 1|1
1 55148456 . G T . . . GT 1|1
1 70504789 . C T . . . GT 1|1
1 167059520 . A T . . . GT 1|1
1 182496864 . A T . . . GT 1|1
1 197073351 . C T . . . GT 1|1
1 216373211 . G T . . . GT 1|1
10 37490170 . G A . . . GT 1|1
10 56089432 . A C . . . GT 1|1
...
[cocodong@biocluster ~/]$ icages.pl input.vcf
BED input with one sample with his/her somatic structural variations only
If you only have BED files for all structural variations detected in this patient with reference genome version hg19, iCAGES can also automatically detect the input format of your data and carry on downstream analysis. This exemplary input file is also provided in iCAGES package.
[cocodong@biocluster ~/]$ head input.bed
chr12 85865797 85887628
chr20 15052592 15071191
chr16 87340388 87349798
chr2 213000509 213007522
[cocodong@biocluster ~/]$ icages.pl input.bed