Hi I'm a new to bioinformatics.
I have a task to analyze WES data using ABSOLUTE R package. I must use ABSOLUTE for that task although there are several tools for the same purpose.
What I found are ABSOLUTE takes an output from HAPSEG or an user-segmented file as input, (http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE/1)
and HAPSEG takes a SNP file as input only from the result of SNP_250K_STY or SNP_6.0 microarray (Affymetrix). (http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/HAPSEG/)
But what I want to analyze are WES data from llumina Hiseq2000.
Is there method to convert these WES data to SNP file for HAPSEG input or user-segemented file for ABSOLUTE input?