| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/unified_genotyper/gatk_unified_genotyper/0.0.6 (this tool) |
| gatk_unified_genotyper |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| gatk | 1.4 | package |
| samtools | 0.1.18 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
gatk_param_type|gatk_param_type_selector: basic analysis_param_type|max_deletion_fraction: -1 rod_bind_0|rod_bind_type|rod_bind_type_selector: dbsnp analysis_param_type|compute_SLOD: False analysis_param_type|output_mode: EMIT_ALL_CONFIDENT_SITES analysis_param_type|indelGapOpenPenalty: 3 analysis_param_type|analysis_param_type_selector: advanced rod_bind_0|rod_bind_type|input_rod: gatk/fake_phiX_variant_locations.vcf reference_source|ref_file: phiX.fasta analysis_param_type|min_indel_count_for_genotyping: 2 analysis_param_type|min_base_quality_score: 17 analysis_param_type|genotyping_mode_type|genotyping_mode: DISCOVERY analysis_param_type|indel_heterozygosity: 0.000125 reference_source|reference_source_selector: history genotype_likelihoods_model: BOTH analysis_param_type|pcr_error_rate: 0.0001 analysis_param_type|p_nonref_model: EXACT analysis_param_type|doContextDependentGapPenalties: False standard_min_confidence_threshold_for_emitting: 4 analysis_param_type|indelGapContinuationPenalty: 10 reference_source|input_bams_0|input_bam: gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam standard_min_confidence_threshold_for_calling: 0 analysis_param_type|heterozygosity: 0.001 analysis_param_type|indelHaplotypeSize: 80 |
output_vcf: gatk_unified_genotyper_out_1.vcf output_metrics: gatk_unified_genotyper_out_1.metrics output_log: gatk_unified_genotyper_out_1.log.contains |
gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam phiX.fasta gatk/fake_phiX_variant_locations.vcf gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains |