Hi everyone.

I'm calling some variants using samtools (and bcftools) from a bwa aligned and sorted BAM.

For some reason, the samtools mpileup is reporting all zero quality scores, but I know the base and read quality scores in the BAM are good (viewed in IGV)

<img alt="" src="http://i.imgur.com/c6pUcby.png" style="height:781px; width:308px" />

    samtools mpileup -uvB -t DP -f ref.fa -r chrX:48,902,600-48,902,700 mapped_sorted.bam

gives me

```
CHROM    POS    ID    REF    ALT    QUAL
chrX    48902600    .    C    <X>    0
..
```

One for every base in the specified range

Here's a variant position:

    chrX    48902688    .    A    C,<X>    0

Base phred quality scores as reported in IGV range from 20-40 and read mapping quality is all 60.

Anyone run into this before?

Thanks!
I also spent last week or so trying to work through the project on calling variants and identifying causative gene (plants have been selected through phenotype. haven't finished the projects yet). I don't understand exactly what happens behind the scene, but `samtools mpileup` doesn't call variants! You need to use `bcftools call` to call variants. Here is some what helpful link http://samtools.sourceforge.net/mpileup.shtml Except be wary because it is out of date, bcftools have changes since that ti,me and you need to use `bcftools call` instead of `view`. Here is what I did to get my VCF files with quality scores

    for i in Bams/*.bam; do (samtools mpileup -g -f reference.fa $i | bcftools call -c -v - > calledVCF/$(basename $i .bam).vcf)& done