It's not too difficult to generate a bed file of GC content along the genome. You just need the reference fasta file and a genome file giving the length of the chromosomes. Then with bedtools, first create sliding windows along the genome and for each window calculate the %GC, then use e.g. awk to get rows where %CG is above/below a threshold, something like:

bedtools makewindows -g hg19.genome -w 1000 \
| nucBed -fi hg19.genome.fasta -bed \
| awk '$5 > 0.9 || $5 < 0.1'

See 'nucBed -h' for the output format, I think %GC is going to be in column 5, not sure though.