comparison gatk4_Mutect2.xml @ 5:53ce8be43212 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 commit a786695a05177842dcc89ef6bb21b38d7e7ce2db"

4:1cea23583655

variants include single nucleotide (SNV) and insertion and deletion
(indel) variants. The caller combines the DREAM challenge-winning
somatic genotyping engine of the original MuTect (`Cibulskis et al.,
2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
with the assembly-based machinery of
`HaplotypeCaller <https://www.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php>`__.

This tool is featured in the *Somatic Short Mutation calling Best
Practice Workflow*. See
`Tutorial#11136 <https://software.broadinstitute.org/gatk/documentation/article?id=11136>`__
for a step-by-step description of the workflow and
`Article#11127 <https://software.broadinstitute.org/gatk/documentation/article?id=11127>`__
for an overview of what traditional somatic calling entails. For the
latest pipeline scripts, see the `Mutect2 WDL scripts
directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
Although we present the tool for somatic calling, it may apply to other
contexts, such as mitochondrial variant calling.

5:53ce8be43212

variants include single nucleotide (SNV) and insertion and deletion
(indel) variants. The caller combines the DREAM challenge-winning
somatic genotyping engine of the original MuTect (`Cibulskis et al.,
2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
with the assembly-based machinery of
`HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.

This tool is featured in the *Somatic Short Mutation calling Best
Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__
for an overview of what traditional somatic calling entails, with usage examples. For the
latest pipeline scripts, see the `Mutect2 WDL scripts
directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
Although we present the tool for somatic calling, it may apply to other
contexts, such as mitochondrial variant calling.