I am trying to call SNPs from ChIP-seq data and currently, I'm using samtools mpileup for this. I am wondering however whether mpileup's SNP calling is affected by the assumption that we have individual-level genomic data and therefore all observed deviations in read count from the 1:1, or 0:1/1:0 ratios can only arise due to technical bias. Could anyone comment?
I know GATK has an RNA-seq SNP-calling module which should in theory account for this. Has anyone tried using it with ChIP-seq?