jacmarjorie
commented
8 years ago Ideally, the MAF resource TSV would have the following columns from which I could inherit the columns I need (naming conventions aside):
| individual_id | normal_sample_id | tumor_sample_id | maf_resource_id |
|---|
As a Variant Store consumer of a project's individual, sample, and resource (MAF) tsv's I need a consistent naming and organization to simplify access to each of these project's TSVs in order to build a CallSet resource that is identifiable by ES and read into the Kibana interface.
Right now, this is the structure I see for project organization in the logstash directory:
└── logstash ├── README.md ├── baml │ ├── BeatAML_Data_Source.xlsx │ ├── BeatAML_rnaseq_2015_10_20_public_dashboard.xlsx │ ├── BeatAML_seqcap_2015_10_20_public_dashboard.csv │ ├── BeatAML_seqcap_2015_10_20_public_dashboard.tsv │ ├── BeatAML_seqcap_2015_10_20_public_dashboard.xlsx │ ├── Diagnosis_Labs_Treatments_Outcomes_2015_10_27.xlsx │ ├── baml-dataset.conf │ ├── baml-individual.conf │ ├── baml-resource.conf │ ├── baml-specimen.conf │ ├── dataset.tsv │ ├── default_index_template.json │ ├── dna-resources.tsv │ ├── individual.tsv │ ├── resource.tsv │ └── specimen.tsv ├── denormalizer │ ├── Dockerfile │ ├── README.md │ ├── aggregated_resource.py │ └── requirements.txt ├── example-data │ ├── README.md │ └── icgc │ └── icgc-dataset-1446768311064 │ ├── donor.tsv │ ├── donor_exposure.tsv.gz │ ├── donor_family.tsv.gz │ ├── donor_therapy.tsv.gz │ ├── sample.tsv │ ├── specimen.tsv │ ├── ssm_open-truncate.tsv │ └── ssm_open.tsv.gz ├── icgc │ ├── default_index_template.json │ ├── donor.tsv │ ├── icgc-donor.conf │ ├── icgc-resource.conf │ ├── icgc-sample.conf │ ├── icgc-specimen.conf │ ├── sample.tsv │ ├── specimen.tsv │ └── ssm_resources.tsv ├── june_demo │ ├── Austin │ │ ├── genome_data.tsv │ │ ├── images.tsv │ │ ├── projects.tsv │ │ └── specimens.tsv │ ├── OHSU-Data.xlsx │ ├── Portland │ │ ├── genome_data.tsv │ │ ├── images.tsv │ │ ├── projects.tsv │ │ └── specimens.tsv │ ├── ThirdSite │ │ ├── genome_data.tsv │ │ ├── images.tsv │ │ ├── projects.tsv │ │ └── specimens.tsv │ ├── datasets.tsv │ ├── deleteIndexes.sh │ ├── individual.tsv │ ├── ohsu-datasets.conf │ ├── ohsu-individual.conf │ ├── ohsu-specimens.conf │ └── specimens.tsv └── start_logstash.sh