Question: Somatic and Germline variant calling in ion torrent
gravatar for inayat45shaikh
5.1 years ago by
inayat45shaikh40 wrote:


We have data of tumor (Tissue) and Normal (Blood) control from the same patients. We want to call somatic and germline variants in the same individual.

To achieve this, We aligned Tumor and normal sample each separately with hg19 and called variants. For identification of somatic mutations, we compare mutations of both sample together and, mutations occurring only in tumor sample was considered to be somatic. Now for germline detection, we considered all mutations identified in Normal sample.

Is this the Wright approach for Somatic and germline identification from the same individual? or any suggestions?


snp alignment • 3.1k views
ADD COMMENTlink modified 4.5 years ago by graeme.grimes10 • written 5.1 years ago by inayat45shaikh40
gravatar for TriS
4.7 years ago by
United States, Buffalo
TriS4.3k wrote:

example of (some of the) tools to do what Sean mentioned are VarScan2, MuTect, Strelka and SomaticSniper

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by TriS4.3k
gravatar for Sean Davis
4.7 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Generally, you'll want to use a variant caller that considers the tumor and normal samples simultaneously. A google search for somatic variant caller will get you a starting list.

ADD COMMENTlink written 4.7 years ago by Sean Davis26k
gravatar for inayat45shaikh
4.6 years ago by
inayat45shaikh40 wrote:

Thanks Sean, for the response..... can you suggests some software's I have a question, are these softwares takes input raw files or aligned bam files, i dont know about the idea of calling variants from tumor and normal raw files, but i do know little bit about calling variants from aligned bam files. Please correct me if i am wrong, generally BAM file is used to call SOMATIC variants by searching variants only in tumor sample and not in the control and rest of the variants is considered as GERMLINE. if this is the case then how getting variants from each sample separately and then classify it into GERMLINE and SOMATIC, is different from the tumor and normal sample comparison simultaneously.?

ADD COMMENTlink written 4.6 years ago by inayat45shaikh40
gravatar for graeme.grimes
4.5 years ago by
graeme.grimes10 wrote:

I agree with Sean you need to use a joint variant caller.

You could use Thermo's own Ion Torrent, cloud based, Variant caller, Ion Reporter,

Information on Tumor-Normal pair workflows can be found here.

I think you get 10Gb of storage with the free account.

ADD COMMENTlink written 4.5 years ago by graeme.grimes10
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