Gene Variant Data in VCF format is loaded from VCFDataToUpload directory. VCF data loading with transmart-data is described on tranSMART wiki
VCF data file is just that - gene variant data in VCF format generated as an output of a gene variant software package such as PLINK. One should not attempt to open a vcf format data file with any text editing desktop apps. This breaks the format and the file can’t be loaded.
vcf Data (sample)
Unlike Mapping files for HDD data, vcf data mapping file includes two comment lines.
#STUDY_TITLE: Complete Genomics_Breast Cancer
|Tumor_Blood_Pair1||1||Biomarker_Data+ Single_Nucleotide_Polymorphism+ Variant_Call_Format_(VCF)|
|Tumor_Blood_Pair2||2||Biomarker_Data+ Single_Nucleotide_Polymorphism+ Variant_Call_Format_(VCF)|