It's not currently part of
batch, so I'd recommend running it in a loop in Bash or a Makefile.
No variation, or no reads? The latter would be an issue with mapping, the former maybe not. Which chromosomes or regions are causing trouble? I'd expect that regions close to centromeres and telomeres, as well as chr6 and chrY, would be noisy. Using more samples in your pooled reference can help to both reduce noise at these regions and improve the sensitivity of calling in the rest of the genome.
In the .cns data it looks like very low variation, but when mapped to a diagram the gene names do not show up and the sections are blank. I'm missing a section of chromosome 15, 14, and X. The sample size is currently around 30, maybe increasing would help. The missing sections are consistent for each sample.