Miscellaneous |
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 |