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The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
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
Tagged:
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