Created
November 3, 2015 18:28
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Adding chr to a GTF file
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| awk '{ if($1 !~ /^#/){print "chr"$0} else{print $0} }' Homo_sapiens.GRCh37.75.gtf |
This will add chr in front of every line, irrespective of what's on that line, though....
Thank you!
Thanks. For avoiding non-chromosomal regions, like repeats or mitochondrial, I just added an "or" (pipe) [A-Z ] to the regex:
/^#|[A-Z]/
These regions usually start with a capital letter instead of a number.
X and Y would be excluded with that. Instead, you can use this:
awk '{ if($1 ~ /^[0-9]+$/ || $1 ~ /^(X|Y)$/){print "chr"$0} else{print $0} }' yourfile.gtf
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Thanks.It worked.