Analysis of unmatched tumor sample

[michelle-jahja]

Hi, based on your vignette in README, the analysis included a matched normal along with unmatched BAMS to process the tumor snp-pileup. If my samples do not have a matched normal, is it as simple as not adding --normal-bam Normal.bam as an argument in the tumor pileup? Following this, how would the arguments for readSnpMatrix and preProcSample and other downstream functions change? I don't fully understand the difference between the arguments MandUnormal and unmatched. Would this both be FALSE for an unmatched sample?

Thank you and would be grateful for any advice on this analysis.