| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_validate/2.8.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_validate/0.0.7 |
| gatk2_variant_validate |
| 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 dbsnp_rod_bind_type|dbsnp_rod_name: dbsnp reference_source|reference_source_selector: history do_not_validate_filtered_records: None dbsnp_rod_bind_type|dbsnp_rod_bind_type_selector: set_dbsnp reference_source|input_variant: gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf dbsnp_rod_bind_type|dbsnp_input_rod: gatk/fake_phiX_variant_locations.vcf warn_on_errors: True reference_source|ref_file: phiX.fasta |
output_log: gatk_validate_variants_out_1.log.contains |
gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf phiX.fasta gatk/fake_phiX_variant_locations.vcf gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains |