SELECT¶
The SELECT command allows you to choose which columns to show from the source by entering a comma-delimited list.
When selecting in GOR, genomic ordered relational data is expected, so it is mandatory to have a CHROM and POS as the first two columns. However, when the SELECT statement is used in NOR, you can choose whatever columns you want. If columns other than the first two (e.g. #1 and #2) are selected to become the first two columns, care must be taken to ensure that proper genomic order is preserved (see discussion on the -ir option in the JOIN command).
See also the SELWHERE command.
Usage¶
gor ... | SELECT < columns >
Examples¶
The following example shows a SELECT command that includes many different types of notation.
gor ... | SELECT 1,2,#3-#5,Cola,7-Colb,Info*,Cola[+1]-Colg[-1],Colm-
Included in this SELECT are: columns 1, 2, 3 through to 5, a column named Cola, columns from 7 up to Colb, any column starting with ``Info,the column right after Cola up to the column right before Colg, and from Colm onwards to the end of the column list.
Frequently, the SELECT command is used to limit the number of columns returned by the query. In the following example, we are retrieving only those columns that define the variant calls from the whole genome sequencing variants table:
gor source/var/wgs_varcalls.gord
| select chrom,pos,reference,call
| distinct
| top 100