Repository revision
4:1cea23583655

Repository 'gatk4_mutect2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2

GATK4 Mutect2 tool metadata
Miscellaneous
- Call somatic SNVs and indels via local assembly of haplotypes
gatk4_mutect2
toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy0
4.1.7.0+galaxy0
gatk SortSam --version 2>&1 | grep Version | cut -d ':' -f 2
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy02
toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.4.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.4.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.4.0+galaxy0
gatk4_mutect2
Requirements (dependencies defined in the <requirements> tag set)
name version type
gatk4 4.1.7.0 package
tabix 0.2.5 package
samtools 1.9 package
Functional tests
name inputs outputs required files
Test-1 optional|optional_parameters: no
reference_source|reference_sequence: reference.fa
mode|tumor: Mutect2-in1.bam
advanced|advanced_parameters: no
reference_source|reference_source_selector: history
mode|mode_parameters: tumor_only
outputs|output_parameters: no
gzipped_output: False
attributes: name
Mutect2-in1.bam
reference.fa
name
Test-2 optional|optional_parameters: no
reference_source|reference_sequence: reference.fa
mode|tumor: Mutect2-in2.bam
advanced|advanced_parameters: no
reference_source|reference_source_selector: history
mode|mode_parameters: tumor_only
outputs|output_parameters: no
gzipped_output: False
attributes: name
Mutect2-in2.bam
reference.fa
name
Test-3 optional|optional_parameters: yes
optional|annotation: ['StrandBiasBySample', 'BaseQualityHistogram', 'OrientationBiasReadCounts']
mode|tumor: Mutect2-in3.bam
advanced|advanced_parameters: no
reference_source|reference_source_selector: history
mode|mode_parameters: tumor_only
outputs|output_parameters: no
reference_source|reference_sequence: reference.fa
optional|annotation_group: StandardMutectAnnotation
gzipped_output: False
attributes: name
Mutect2-in3.bam
reference.fa
name
Test-4 optional|optional_parameters: no
reference_source|reference_sequence: hg38
mode|tumor: Mutect2-in4.bam
advanced|advanced_parameters: no
reference_source|reference_source_selector: cached
mode|mode_parameters: tumor_only
outputs|output_parameters: no
gzipped_output: False
attributes: name
Mutect2-in4.bam
name
Test-5 optional|optional_parameters: no
reference_source|reference_sequence: reference.fa
mode|tumor: Mutect2-in5.bam
advanced|advanced_parameters: no
reference_source|reference_source_selector: history
mode|mode_parameters: tumor_only
outputs|output_parameters: yes
outputs|debug_bam: True
outputs|debug_assembly: True
outputs|debug_activity: True
gzipped_output: False
attributes: name
attributes: name
attributes: name
Mutect2-in5.bam
reference.fa
name
Test-6 optional|optional_parameters: no
reference_source|reference_sequence: chr20.fa
mode|tumor: tumor.bam
advanced|advanced_parameters: no
reference_source|reference_source_selector: history
mode|mode_parameters: somatic
outputs|output_parameters: no
mode|normal: normal.bam
gzipped_output: False
attributes: name
tumor.bam
normal.bam
chr20.fa
name