questions about the cell lines whole genome sequencing

Question

[SeqNewbie]

Hi everyone, I am doing whole genome sequencing on several cancer cell lines. When I want to analyze the wgs data, I don't know how to do variant filtering when no normal tissues are available for most of the cell lines. How many variants are there after mapping and variant calling against to the reference genome? How about filtering common variant from 1000GENOME, dbSNP or other sequencing normal samples?

[Sam]

It really depends on what you are looking for. If you are looking for rare variants, then you should try to filter out the common variants. It is very important for you to tell us what you are trying to do or else it is difficult for us to answer

[SeqNewbie]

sorry. For cancer samples sequencing, normal tissues are used to remove germline mutation. We can get "somatic mutations". But we have no normal tissues for most of the cancer cell lines. We can use variants found in normal tissues, such as 1000GENOME, to do a similar filter. I don't konw what the results will be for the two filter methods.