Picard CollectGcBiasMetrics ignoring certain chromosomes/sequences
The proper solution is to use a different tool (some of this you could do with computeGCBias in deepTools). But since you don't want to do that, you'll have to manually remove unwanted chromosomes from the BAM file(s):

$ cat foo.awk
BEGIN{split(excludes, excludeList, " ")}
{exclude=0
if($1 == "@SQ") {
    for(ex in excludeList) {
        if(ex == substr($2, 4)) {
            exclude=1
            break
        }
    }
} else { \
    for(ex in excludeList) {
        if(ex == $3) {
            exclude=1
            break
        }
    }
}
if(!exclude) print}

$ excludes="chr1 chr2"
$ samtools view -h alignments.bam | awk -v excludes="$excludes" -f foo.awk | samtools -bo alignments.filtered.bam


The awk script is stripping unwanted chromosomes from the header and the body. You can then run the result through picard.