I want to count number of the variants called on each chromosome for each sample from a multi sample vcf file.
Any help would be really appropriated.
Thanks 
Ram 
Split your vcf file by sample and count how many times chromosom appear in each file .

    FILE=yourfile.vcf
    for sample in `bcftools query -l $FILE`
    do 
    	  bcftools view -c1 -H -s $sample -o ${sample}.vcf $FILE
    	  cat ${sample}.vcf |cut -f1|uniq -c > ${sample}.count
    done