The awk script makes me confused

[lyhonk]

I think the awk script you given has some mistakes awk '{if($1 ~ "^#") {gsub("contig=<ID=", "contig=<ID=chr"); gsub("contig=<ID=chrMT", "contig=<ID=chrM"); print} else gsub("^MT", "M"); print "chr"$0}' mgp.v5.merged.snps_all.dbSNP142.vcf I think this script should be this awk '{if($1 ~ "^#") {gsub("contig=<ID=", "contig=<ID=chr"); gsub("contig=<ID=chrMT", "contig=<ID=chrM"); print} else {gsub("^MT", "M"); print "chr"$0}}' mgp.v5.merged.snps_all.dbSNP142.vcf my system is centos 7

[FelixKrueger]

Thanks for the pointer, I've added the squiggly brackets.