ask for help about TCGA mutation data

[尹超艺]

Dear cBioPortal community,

I would like to ask you for a rather general question regarding the utilization of mutational MAF cancer files from varscan somatic type.I want to incorporate information on the bases immediately 5’ and 3’ to each mutated base generating 96 possible mutation types (6 types of substitution( C>A, C>G, C>T, T>A, T>C, and T>G) x 4 types of 5’ base x 4 types of 3’ base.But when using mut.to.sigs.input in package deconstructSigs, I have some questions. Data has Reference_Allele column , Tumor_Seq_Allele1 column and Tumor_Seq_Allele2 column. So, which column should I choose for my reference base and my alteration base? The Reference_Allele column is not exactly the same as the Tumor_Seq_Allele1 column.

   Hugo_Symbol Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
[1,] "PITPNM3"   "chr17"    "6471346"      "6471346"    "A"              "A"               "C"              
[2,] "TP53"      "chr17"    "7675094"      "7675094"    "A"              "C"               "C"              
[3,] "MYH2"      "chr17"    "10537747"     "10537747"   "T"              "T"               "C"              
[4,] "FLOT2"     "chr17"    "28882662"     "28882662"   "C"              "C"               "A"              
[5,] "MYO1D"     "chr17"    "32775895"     "32775896"   "-"              "-"               "CATAT"          
[6,] "MYO1D"     "chr17"    "32775901"     "32775910"   "GGGTCACCCT"     "GGGTCACCCT"      "-"    

Thanks. I am looking forward to your reply. I really appreciate your help.

Chaoyi Yin

	尹超艺
yinch...@163.com