Mercurial > repos > iuc > gatk4_mutect2

comparison gatk4_Mutect2.xml @ 6:04253ade1697 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 commit a786695a05177842dcc89ef6bb21b38d7e7ce2db"
author iuc
date Wed, 06 Oct 2021 12:04:04 +0000
parents a39dba5ba783
children 91d37702c47b
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5:a39dba5ba783 6:04253ade1697
697 variants include single nucleotide (SNV) and insertion and deletion 697 variants include single nucleotide (SNV) and insertion and deletion
698 (indel) variants. The caller combines the DREAM challenge-winning 698 (indel) variants. The caller combines the DREAM challenge-winning
699 somatic genotyping engine of the original MuTect (`Cibulskis et al., 699 somatic genotyping engine of the original MuTect (`Cibulskis et al.,
700 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__) 700 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
701 with the assembly-based machinery of 701 with the assembly-based machinery of
702 `HaplotypeCaller <https://www.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php>`__. 702 `HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.
703 703
704 This tool is featured in the *Somatic Short Mutation calling Best 704 This tool is featured in the *Somatic Short Mutation calling Best
705 Practice Workflow*. See 705 Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__
706 `Tutorial#11136 <https://software.broadinstitute.org/gatk/documentation/article?id=11136>`__ 706 for an overview of what traditional somatic calling entails, with usage examples. For the
707 for a step-by-step description of the workflow and
708 `Article#11127 <https://software.broadinstitute.org/gatk/documentation/article?id=11127>`__
709 for an overview of what traditional somatic calling entails. For the
710 latest pipeline scripts, see the `Mutect2 WDL scripts 707 latest pipeline scripts, see the `Mutect2 WDL scripts
711 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__. 708 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
712 Although we present the tool for somatic calling, it may apply to other 709 Although we present the tool for somatic calling, it may apply to other
713 contexts, such as mitochondrial variant calling. 710 contexts, such as mitochondrial variant calling.
714 711