variant calling on ChIP-seq style data: samtools mpileup with minimal filters
I used this in the past for ChIP-seq data and it generated SNVs:

samtools mpileup \
--uncompressed --max-depth 10000 --min-MQ 20 --ignore-RG --skip-indels \
--fasta-ref ref.fa file.bam \
| bcftools call --consensus-caller \
&gt; out.vcf


This was samtools 1.3 in case that makes a difference.