Averaging multiple IgG BAM files for use as a control in ChromHMM

Question

[luminea]

Hello, I have three BAM files from Cut&Tag experiments using IgG (negative control). I would like to use them as a common control for several histone marks in a ChromHMM analysis. Instead of using the three BAM files separately, I want to create a single BAM file that represents the average or merged signal from the three IgG datasets to get a more robust estimate of the background. Is there any recommended method or tool to do this kind of averaging or merging directly from BAM files?

Thank you for your help

[GenoMax]

samtools merge will merge multiple BAM files into one --> https://www.htslib.org/doc/samtools-merge.html

See if Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM? helps with your question.

[ATpoint]

BAM files do not contain counts or an "average-able" metric so I would simply merge the files indeed, maybe after subsampling to the same read count to have it a bit "more fair".