Has anyone used Sicer to peak call using bam files and bed files. I would appreciate it if someone could help me get the command to do peak calling using treatment vs input bam files. Also, how does sicer use bed files to peak call, i thought peak calling was produced bed files. Would appreciate any help.
Have you read the manual? It gives very clear commands as for how to run with a control file (or without):
sicer -t treatment.bam -c control.bam -s hg38 -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 -g 600 -e 1000
Those are the default parameters. You can supply the reads in either bam or BED format. Having aligned reads in BED format isn't too uncommon.
The output files are in BED-like format, you can read more about them here.