I post a question continuously.
In this question , curious things are about somatic and germline.
Please see the below paragraph with bold text.
At every position where one or both samples had a variant, VarScan performs a direct comparison between tumor and normal genotype and supporting read counts to determine the somatic status. (I do understand so far but next sentence is confused to me)
Variants present in both samples are classified as somatic , variants heterozygous in the normal but homozygous in the tumor are classified as LOH(loss of heterozygosity) , and variant shared between samples are classified as germline.
the second sentence above, What is the difference between somatic and germline?
The sentence that Variants present in both samples are confused in meaning. I knew that somatic mutation is that the variants only exist in tumor sample, but reading and thinking again that sentence .., I can't connect the somatic concept i already knew.
and also i post a question before , but re-question about homozygous and heterozygous.
how can we define homo or hetero considering we have a only one pair of chromosome ?
I can't imagine the homo or hetero in next-seq , because i knew that the only one pair of chromosomes is sequenced...
Am i misunderstanding about concept?
I hope you understand my fuzzy questions.
I am looking forward to your answer