| MuTect2 is a somatic SNP and indel caller that combines the DREAM challenge-winning somatic genotyping engine of the original MuTect with the assembly-based machinery of HaplotypeCaller. The MuTect2 wrapper mirrors the IUC wrapper https://github.com/galaxyproject/tools-iuc/blob/master/tools/gatk4/gatk4_Mutect2.xml. However, appropriate code changes are made in the original wrapper in order to expose parameters or outputs required to run the FilterMutectCall wrapper. FilterMutectCall applies filters to the raw output of Mutect2. see https://gatk.broadinstitute.org/hc/en-us/articles/4409917406107-FilterMutectCalls#--reference for details. Parameters are contained in M2FiltersArgumentCollection and described in https://github.com/broadinstitute/gatk/tree/master/docs/mutect/mutect.pdf. |
hg clone https://toolshed.g2.bx.psu.edu/repos/artbio/gatk4
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Merge the stats output by scatters of a single Mutect2 job | 4.1.7.0+galaxy3 | 21.01 | |
| - Call somatic SNVs and indels via local assembly of haplotypes | 4.1.7.0+galaxy3 | 21.01 | |
| Filter variants in a GATK4 Mutect2 VCF callset | 4.1.7.0+galaxy3 | 21.01 | |