running a samtools command for multiple bam files from 1000 genomes project
The command you're looking for is:

samtools view -c http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam 2:1000000-2000000


For a series of intervals, you'd be better off scripting something with pysam:

import pysam
bam = pysam.AlignmentFile("some file.bam")
regions = open("your regions.bed")
for region in regions:
    chrom, start, end = region.split("\t")
     bam.count(chrom, int(start), int(end))  # Do something with the result


You might see if there are bigWig files available, they'd be faster to process.