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