Regselect

Format

cg regselect file region_select_file ?near?

Summary

select all regions or variants in file that overlap with regions in region_select_file

Description

Regions files are tab separated files that contain regions using the columns chromosome, begin, end. Regions must be sorted. regselect selects all regions or variants in file that overlap with regions in region_select_file. The resulting regions files is written to stdout.

Arguments

file: regions file, if - is given, data will be piped from stdin
region_select_file: selection regions file
near: if present, must be a number. Selection regions will be extended (to both sides) with the given amount of bases.

You can also run the command from stdin by only giving one parameter (dropping the file parameter, the remaining parameter will be used as region_select_file)

Options

-o outputfile: write to outputfile instead of stdout
-near number: same a near argument, but as option

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