Question: Somatic mutation(indels) in blood sample(autism)
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gravatar for lee.jingu0626
4.4 years ago by
Korea, Republic Of
lee.jingu062630 wrote:

Hi.

I have two questions about the somatic mutation.

1. I researched the somatic mutation(indels) in cancer sample. And now I want to detect the somatic indels in blood sample(autism). However it is hard to find the somatic indels because it is blood sample.

In cancer sample there are two types of samples like normal sample and tumor sample but in blood sample for autism there is only one type of sample. (Blood sample is undistinguished)

So how can I get the somatic indels in blood sample?

2. Also I wonder the detailed principle for detecting the somatic mutation in VarScan2 and Scalpel.

 

Thanks.

autism mutation blood somatic indel • 1.9k views
ADD COMMENTlink written 4.4 years ago by lee.jingu062630

Varscan and Scalpel require tumor-normal pair data to detect somatic mutations (just as any other software when the task is detection of somatic mutaions). In case of tumor only (or blood in your case), the task is the following: find all mutations (you can use the simplest GATK or samtools workflows for this purpose) and flag known mutations from cosmic and dbSNP. Detection of the de novo somatic mutatinons with only blood sample is impossible. Look this post for more details Discrimination Between Germline And Somatic Mutations In Tumor Without The Availability Of The Normal Paired Sample.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Max Ivon120
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