text: user1771: 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) but it seems it is not yet ready for production. Which alternative tools do you suggest?
  
  user964: 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 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.
  
original_text: 1771: <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>
   964: <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>
  