| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/jjohnson/ensembl_variant_report/ensembl_variant_report/0.4.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/jjohnson/ensembl_variant_report/ensembl_variant_report/0.3.0 |
| toolshed.g2.bx.psu.edu/repos/jjohnson/ensembl_variant_report/ensembl_variant_report/0.2.0 |
| toolshed.g2.bx.psu.edu/repos/jjohnson/ensembl_variant_report/ensembl_variant_report/0.1.0 |
| ensembl_variant_report |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| gtf_to_genes | 1.40 | package |
| twobitreader | 3.1.7 | package |
| biopython | 1.70 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
ref|ref_file: GRCh38_X.2bit ref|ref_source: history gtf_file: GRCh38_X.83.gtf variant|input_vcf: GRCh38_X400k_ANN.vcf variant|fmt: vcf |
attributes: name |
GRCh38_X400k_ANN.vcf GRCh38_X.2bit GRCh38_X.83.gtf name |
| Test-2 |
ref|ref_file: GRCh38_X.2bit ref|ref_source: history gtf_file: GRCh38_X.83.gtf variant|input_vcf: GRCh38_X400k_EFF.vcf variant|fmt: vcf |
attributes: name |
GRCh38_X400k_EFF.vcf GRCh38_X.2bit GRCh38_X.83.gtf name |
| Test-3 |
ref|ref_source: history report|readthrough: 1 variant|fmt: vcf variant|input_vcf: GRCh38_X400k_ANN.vcf gtf_file: GRCh38_X.83.gtf ref|ref_file: GRCh38_X.2bit |
attributes: name |
GRCh38_X400k_ANN.vcf GRCh38_X.2bit GRCh38_X.83.gtf name |
| Test-4 |
ref|ref_source: history filter|min_depth: 100 variant|fmt: vcf variant|input_vcf: GRCh38_X400k_ANN.vcf filter|min_freq: .80 gtf_file: GRCh38_X.83.gtf ref|ref_file: GRCh38_X.2bit |
attributes: name |
GRCh38_X400k_ANN.vcf GRCh38_X.2bit GRCh38_X.83.gtf name |
| Test-5 |
variant|input_tsv: GRCh38_X400k.tsv ref|ref_source: history variant|pos_column: 2 variant|fmt: tsv gtf_file: GRCh38_X.83.gtf variant|alt_column: 4 variant|transcript_column: 7 variant|dpr_column: 9 ref|ref_file: GRCh38_X.2bit variant|dp_column: 8 variant|ref_column: 3 |
attributes: name |
GRCh38_X400k.tsv GRCh38_X.2bit GRCh38_X.83.gtf name |