Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently.
All of these three formats are tab-separated files, so basically the following should work. I feel weird about it since most people I know don't use MySQL to work with these files.
LOAD DATA LOCAL INFILE 'bed.bed' INTO TABLE bed-file FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n' IGNORE 1 ROWS (list of the columns) SET creation_date = STR_TO_DATE(@creation_date, '%m/%d/%y');