I have a bed file (tab separated columns) with hundreds of genomic coordinates as follows.
chr1 88833393 88834022 EXr19 1 + chr1 22531002 22531628 EXr20 1 + chr1 10355070 10355696 EXr21 1 +
I am trying to query a gemini database by using a genomic region based query as follows.
gemini query --header --show-samples --region 1:88833393-88834022 -q "select * from variants" gemini.db >> output.tsv
Is there a way I can generate a query for each genomic coordinate given in the bed file automatically? An urgent help will be appreciated.