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MUTECT2 vs MUTECT1
Hello,
We are using MUTECT to call somatic variants in cancer
thus far we were using MUTECT1
It works fast, however it does not call indels.
New MUTECT2 in GATK 3.5 calls both point mutations and indels.
The only problem that we have with Mutect2 is that it is much slower (20-50 times) than Mutect1.
We tried to parallelize it, but it is still super slow.
Maybe you could help us with this issue?
Thanks in advance
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Best Answer
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Sheila
Broad Institute admin
@Serguei
Hi,Yes, MuTect2 is slower that MuTect1 because of the reassembly step. Have a look at this thread for more information. Unfortunately, we really don't have any recommendations for speeding it up now. You can also look into using WDL.
-Sheila
Answers
@Serguei
Hi,
Yes, MuTect2 is slower that MuTect1 because of the reassembly step. Have a look at this thread for more information. Unfortunately, we really don't have any recommendations for speeding it up now. You can also look into using WDL.
-Sheila