Hi all.

I am using mpileup to extract some sequencing information. However, when I tried to run mpileup with below command

    samtools mpileup -C 50 -vu -t DP -t DV -t DPR -t DP4 -f human_g1k_v37.fasta -l ms_TAR22_mpileup.bed TAR22_N_Filtered_Sorted_Makrdup_Readgroup_Realigned_Recal.bam

The results are nothing except head file of VCF.

I think that the problems occur due to the `-l` option because when I removed `-l` options, it works well but the file size was very large to handle. When I chose `-l` option and run it, as I expected, then it failed to generate sequencing information related to `-l` files. I don't know why mpileup command doesn't output anything but its head even though I followed the manual and ran with the latest samtools version(1.2).

For your reference, here is the data inside my bed files.

```
22      24829532        24829532        ADORA2A
18      12449779        12449779        SPIRE1
12      123005948       123005948       RSRC2
12      25398281        25398281        KRAS
12      22354743        22354743        ST8SIA1
7       93055822        93055822        CALCR
2       170374777       170374777       KLHL41
1       158532510       158532510       OR6P1
1       79002163        79002163        PTGFR
```

Help me to get it!
BED files are 0-based, half-open. What that means is that a SNV location needs to have a difference of 1 between the start and end location. In the case of your BED file, the locations appear to be in 1-based, closed coordinates. So, I suspect that mpileup is not using the BED file as you think. Try subtracting 1 from each element in column 2. Finally, make sure that the chromosome names match (including the "chr" or lack thereof).