variant calling on ChIP-seq style data: samtools mpileup with minimal filters I am running samtools mpileup (v1.4) on a bam file with very choppy coverage (ChIP-seq style data). I want to get a first-pass list of positions with SNVs and their frequency as reported by the read counts, but no matter what I do, I keep getting all SNVs filtered out as not passing QC.

What's the magic parameter set for an initial list of SNVs and frequencies?

EDIT: this is a question I posted on "the other" website, but didn't get a reply there.
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.