| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_base_recalibrator/2.8.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_base_recalibrator/0.0.7 |
| gatk2_base_recalibrator |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| gatk2 | not provided | package |
| samtools | 0.1.19 | package |
| picard | 1.56.0 | package |
| GATK2_PATH | not provided | set_environment |
| GATK2_SITE_OPTIONS | not provided | set_environment |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
gatk_param_type|gatk_param_type_selector: basic analysis_param_type|analysis_param_type_selector: basic rod_bind_0|rod_bind_type|input_rod: gatk/fake_phiX_variant_locations.bed reference_source|input_bam: gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam reference_source|reference_source_selector: history rod_bind_0|rod_bind_type|rod_bind_type_selector: dbsnp reference_source|ref_file: phiX.fasta covariates: ['ReadGroupCovariate', 'HomopolymerCovariate', 'MinimumNQSCovariate', 'PositionCovariate'] |
output_recal: gatk_count_covariates_out_1.csv output_log: gatk_count_covariates_out_1.log.contains |
gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam phiX.fasta gatk/fake_phiX_variant_locations.bed gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains |