I have the following code " not mine"

wget -qO- http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp142Common.txt.gz \
    | gunzip -c - \
    | cut -f2,3,4,5,10 - \
    | sort-bed - \
    > hg19.snp142.bed

when I run it on terminal it gave me the following error

sort-bed: command not found

how to fix it?


1 Answer 1


sort-bed is contained in BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit, which can be easily installed following these steps:

  1. Download the current 64-bit package for Linux from Github BEDOPS Releases. 32-bit binaries can be built via source code by adjusting compile-time variables, see here.
  2. Extract the package to a location of your choice. In the case of 64-bit Linux:

    tar jxvf bedops_linux_x86_64-vx.y.z.tar.bz2

    Replace x, y and z with the version number of BEDOPS you have downloaded.

  3. Copy the extracted binaries to a location of your choice which is in your environment’s PATH, e.g. /usr/local/bin:

    cp bin/* /usr/local/bin

    Change this destination folder, as needed.

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