Created
December 11, 2018 01:24
-
-
Save edawson/cbbd83e0a56ed4a5aabe0727c15fad66 to your computer and use it in GitHub Desktop.
Convert a Picard interval list file to a bzip'ed, tabix-indexed BED file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| grep -v "^@" $1 | awk '{print $1"\t"$2"\t"$3"\t"$5}' > $(dirname $1)/$(basename $1 .interval_list).bed && \ | |
| bgzip $(dirname $1)/$(basename $1 .interval_list).bed && \ | |
| tabix $(dirname $1)/$(basename $1 .interval_list).bed.gz |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment