Used in: gor/nor


This manual entry pertains to the CMD command as it is used as a pipe step. CMD allows you to execute operating system commands that return data that you assume is tabular data within GOR queries.

If you are using external command as a source for your data, then it is better to use GORCMD, for genomic-ordered data, and NORCMD, for non-ordered data.

The CMD analysis step supports nested queries such as: gor my.gor | cmd {python <(gor #genes# | where gene_start-gene_stop < 10000)}.

External commands need to be encapsulated between curly brackets, e.g. cmd {command}.


gor ... | CMD {command}



Execute the command within a NOR query.

-s <type>

Specifies that type of source that will be read [BAM, GOR, or VCF]


Tells the command to not send the header.


gor ... | CMD {<>}