add_chr_names.sh

grep '^>' ../GCF_000002035.6_GRCz11_genomic.fna|grep chromosome|grep Primary| perl -ane '{$h{substr($F[6],0,length($F[6])-1)}=substr($F[0],1);}END{open(FILE,"danio_rerio_incl_consequences.wSIFT.gvf");while($line=<FILE>){chomp($line);@F=split(/\s+/,$line);print "NC_0071",11+$F[0],".7\t",join("\t",@F[1..7]),"\t",join(" ",@F[8..$#F]),"\n" if defined($h{$F[0]});}}' > danio_rerio_incl_consequences.wSIFT.chrnames.gvf