BeRT - Extract Comparison

Target release

2.3

Epic

https://gobiiproject.atlassian.net/browse/GE-35

Document status

DRAFT

Document owner

@Deb Weigand

Designer

@Yaw Nti-Addae

Tech lead

 

Developer

@Luke Cook

QA

@Deb Weigand

Objective

Compare the extract files generated from a BeRT test scenario to a known good extract provided by QA

Requirements - what to compare in each of the files (y = compare, n= do not compare)

Dataset.genotype

Dataset.hmp.txt

marker.file

sample.file

summary.file

project.file

Dataset.genotype

Dataset.hmp.txt

marker.file

sample.file

summary.file

project.file

1

ALL rows

ALL rows except: 

  • dnasample_uuid 

  • gdm_germplasm_id 

  • dnasample_id 

  • dnarun_id 

marker_name 

platform_name 

variant_id 

variant_code 

marker_ref 

marker_alts 

marker_sequence 

marker_strand 

marker_primer_forw1 

marker_primer_forw2 

marker_primer_rev1 

marker_primer_rev2 

marker_probe1 

marker_probe2 

marker_polymorphism_type 

marker_synonym 

marker_source 

marker_gene_id 

marker_gene_annotation 

marker_polymorphism_annotation 

marker_marker_dom 

marker_clone_id_pos 

marker_genome_build 

marker_typeofrefallele_alleleorder 

marker_strand_data_read 

marker_id 

marker_clone_id 

marker_allele2 

marker_allele3 

dnarun_name 

germplasm_name 

germplasm_pedigree 

germplasm_type 

dnarun_barcode 

project_name 

project_pi_contact 

project_genotyping_purpose 

project_date_sampled 

project_division 

project_study_name 

experiment_name 

vendor_protocol_name 

vendor_name 

protocol_name 

dataset_name 

germplasm_external_code 

germplasm_species 

germplasm_id 

germplasm_seed_source_id 

germplasm_subsp 

germplasm_heterotic_group 

germplasm_par1 

germplasm_par1_type 

germplasm_par2 

germplasm_par2_type 

germplasm_par3 

germplasm_par3_type 

germplasm_par4 

germplasm_par4_type 

dnasample_name 

dnasample_platename 

dnasample_num 

dnasample_well_row 

dnasample_well_col 

dnasample_trial_name 

dnasample_sample_group 

dnasample_sample_group_cycle 

dnasample_sample_type 

dnasample_sample_parent 

dnasample_ref_sample 

dnasample_uuid 

gdm_germplasm_id 

dnasample_id 

dnarun_id 

do NOT compare

do NOT compare

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Open Questions

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