Tumor_LogR, Tumor_BAF files with multiple tumor samples and single matched normal sample for use with ascat.asmultipcf()?

[agorelick]

Hi,

I am unclear about the workflow for running ascat with multiple tumor bams (with shared ancestry) and a single matched normal bam.

The example on github says ascat.asmultipcf() should begin with this step: ascat.bc = ascat.loadData(Tumor_LogR_file = "Tumor_LogR.txt", Tumor_BAF_file = "Tumor_BAF.txt", Germline_LogR_file = "Germline_LogR.txt", Germline_BAF_file = "Germline_BAF.txt", gender = rep('XX',100), genomeVersion = "hg19")

However, the instructions Extracting logR and BAF from HTS data and running ASCAT only provide an example with a single tumor and paired normal sample to create the Tumor_LogR.txt and Tumor_BAF.txt files. Are we supposed to run the prepareHTS() function for each tumor sample individually against the single matched normal and then merge the results somehow? Is there example code for how this is supposed to be done?

Thanks for any insights!

[zhangzhhcb]

You need to run prepareHTS() for each tumor and merge them together by the format of "chrs pos sample1 sample2...". You could also find example data in the Exampledata folder. Run other steps in the muti-sample workflow using the combined BAF and logR. Thanks.