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some questions about difference between HaplotypeCaller and MuTect2

Recently I have been worked in variant calling using GATK and I have some questions in the process of learning GATK tools.

  1. I’m interested in the essential difference between HaplotyepCaller and MuTect2 or in other words the essential difference between somatic mutation caller and germline mutation caller.Is only the difference in ability for calling low frequency variants?But both HaplotypeCaller and MuTect2 use local assembly engine and I believe they have the same potential for low-frequency variants calling.I also read some PDF files in GATK about HaplotypeCaller and MuTect2 and learned that they have difference in identifying ActiveRegion and sample genotyping but I can’t find detailed description.
  2. When using MuTect2,whether it will do the same operation in both tumor and matched normal sample and then compare the variants callset in T/N samples?
  3. What the difference between germline SNP and somatic SNV in your opinion?Is that if a variant in the germline database or exist in normal samples it will be germline variants,otherwise it will be somatic variants?
  4. Why lots of people use UnifiedGenotyper or HaplotyeCaller for smatic mutation calling in Nature papers?

Could you give me some advice or recommend some useful articles for me?


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