<p>Those will have to be treated as separate analysis.  You can use Mutect or VarScan for the matched samples and the tools listed in the <a href="https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling">other question</a> for the unmatched samples however that means that you won't be able to compare the results easily.  If the inter-sample comparison is important you will have to run all samples as unmatched.  Personally I have used LoFreq for somatic variant detection with some success.  It is very sensitive so the false positive rate can be high depending on how noisy your data is.</p>

CC BY-SA 3.0
2017-12-13T18:49:27.003Z
2017-12-13T18:49:27.003Z
Bioathlete
<p>I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions.</p>

<p>I was looking for GATK best practices (like <a href="https://software.broadinstitute.org/gatk/best-practices/mutect2.php" rel="nofollow noreferrer">this</a>) but it seems it is not yet ready for production. Which alternative tools do you suggest?</p>

CC BY-SA 3.0
2017-12-13T17:59:15.807Z
Have you looked at this question? https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling
Bioathlete
CC BY-SA 3.0
2017-12-13T18:09:14.893Z
@Bioathlete thanks, I actually didn't find that question before. However, I found that question too specific on tumor-only samples. I also have normals so maybe there are better tools?
gc5
<wgs><mutations><somatic><non-coding>
Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?
# Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?

(Asked by: username_0 on 2017-12-13)

I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions.

I was looking for GATK best practices (like [this](https://software.broadinstitute.org/gatk/best-practices/mutect2.php)) but it seems it is not yet ready for production. Which alternative tools do you suggest?

**Tags:** wgs, mutations, somatic, non-coding
> **Comments:**
> **username_1**: Have you looked at this question? https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling  
> **username_0**: @Bioathlete thanks, I actually didn't find that question before. However, I found that question too specific on tumor-only samples. I also have normals so maybe there are better tools?  

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## 1 answers

### Answer by username_1 on 2017-12-13. Score: 1 | Accepted answer

Those will have to be treated as separate analysis. You can use Mutect or VarScan for the matched samples and the tools listed in the [other question](https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling) for the unmatched samples however that means that you won't be able to compare the results easily. If the inter-sample comparison is important you will have to run all samples as unmatched. Personally I have used LoFreq for somatic variant detection with some success. It is very sensitive so the false positive rate can be high depending on how noisy your data is.


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