Add mutect2 - Githubissues

niemasd / ViReflow

An elastically-scaling automated AWS pipeline for viral consensus sequence generation

GNU General Public License v3.0

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Add mutect2 #4

Closed niemasd closed 3 years ago

niemasd commented 3 years ago

According to this study:

According to Table 2:
- m = --mitochondria-mode true
- m_noM = default mutect2 parameters
- m_md_inf = --mitochondria-mode true --f1r2-max-depth 1000000
- m_md_inf_max_af1 = --mitochondria-mode true --f1r2-max-depth 1000000 -max-af 1
According to Figure 2, all of them seem to do the same except m_noM doing worse in Position = 3029
- Thus, I should just use --mitochondria-mode true

niemasd commented 3 years ago

Never mind, it uses Java, which is a pain to use with Reflow because of memory allocation for the JVM. Given that multiple other good variant callers are already supported, I'll close this ticket and maybe revisit it well in the future if there's significant demand. For context, I've already built a Docker image:

https://hub.docker.com/r/niemasd/gatk