This is very basic, still I'll try to put it in very simple way..
There are 2 kinds of mutations, Germline and Somatic. Most of the analysis concerned with cancer use Somatic mutations (You can search why too much importance for Somatic mutations). When a tumor sample is collected for sequencing, along with tumor tissue, we should also collect a normal tissue (blood sample) from the same patient. We use both of these samples for downstream analysis. When calling variants, most of the variant callers use this normal and tumor bam files, so that variants found common in both files are not considered as suspecting ones. Because the variant is present in normal tissue also, it doesn't have anything to do with disease.
I need to put one normal (non-cancer) patient in my sequencing run?
No, you should use a normal tissue (or blood) sample from same patient.
can I download normal.bam from Internet and using it in my variant calling?
No, you can not use a random normal sample for your analysis, because each patient/person is different.
There are some other ways one can handle a tumor data without having a matched normal. You can search this forum for such analysis tips.
modified 2.5 years ago
2.5 years ago by
venu ♦ 6.1k