Replace lowercase characters with - I have an output from vcfutils.pl vcf2fq with specified minimal depth, and it means that nucleotides with not enough depth are lowercase. 
I would like to change them to gaps. I could do it in higher language but I would like to know the solution in bash. 
I have found simple solution to replace all lowercase to uppercase:

awk 'BEGIN{FS=" "}{if(!/&gt;/){print toupper($0)}else{print $1}}' in.fna &gt; out.fna


but I would like to replace lowercase with -. The first row need to be omitted. Could you help me? Thanks
The following sed command will do the trick.

sed -e '/^[^&gt;]/ s/[a-z]/\-/g' in.fna &gt; out.fna

Lines starting with &gt; will be escaped and the lowercase characters will be replaced with - .