Check that your VCFs are not truncated.

check_chrom_size.sh

# chrom sizes in hg19

declare -A sizes
sizes["chr1"]=249250621
sizes["chr2"]=243199373
sizes["chr3"]=198022430
sizes["chr4"]=191154276
sizes["chr5"]=180915260
sizes["chr6"]=171115067
sizes["chr7"]=159138663
sizes["chrX"]=155270560
sizes["chr8"]=146364022
sizes["chr9"]=141213431
sizes["chr10"]=135534747
sizes["chr11"]=135006516
sizes["chr12"]=133851895
sizes["chr13"]=115169878
sizes["chr14"]=107349540
sizes["chr15"]=102531392
sizes["chr16"]=90354753
sizes["chr17"]=81195210
sizes["chr18"]=78077248
sizes["chr20"]=63025520
sizes["chrY"]=59373566
sizes["chr19"]=59128983
sizes["chr22"]=51304566
sizes["chr21"]=48129895

# get 10M from the end

for chr in `seq 1 22` X
do
    x=`echo *chr${chr}.*vcf.gz.tbi`
    if [ -s $x ]
    then
        pos=`expr ${sizes["chr${chr}"]} - 10000000`
        last_pos=`tabix ${x%.tbi} ${chr}:${pos} | awk '{print $2}' | tail -n1`
        if [[ ${last_pos} == "" ]]
        then
            echo ${x%.tbi} may be truncated
        else
            echo ${x%.tbi}, last_pos:${last_pos}, chrom_size: ${sizes["chr${chr}"]}, remaining `expr ${sizes["chr${chr}"]} - ${last_pos}`
        fi
    else
        echo $x does not exist
    fi
done