Indel realignment multiple cancer samples
It is usually suggested to run individually Tumor normal pair files with indel realignment before we continur for checking for contamination.
I have two questions.
in my case for each patient I have multiple samples, at least 3 tumor and 1 normal. Shall I run indel realignment on all of them at the same time? What do you suggest?
the output of the above command will be a single bam file unless we state the -nWayout option, but still for the contamination we have to use the tumor and the normal vcf files separately. Therefore, we have to use the nWayout option in the indel realignment. Is that correct?