Hello, So, currently I want to get variation in the sequence for each individual sample (human cancer sample). I want to compare whether there are any variation among the cancer sample. What I mean is if I compare one cancer sample with others, I want to see if there are any different variation occur.
Can I use mpileup in samtools to call variation for a single sample and then compare the result after that?
I tried to use samtools for all samples in one go but it gives only one list of variation (VCF file). I think that VCF is the common variation occur in cancer sample.