Aligned and filtered (and deduplicated if applicable) reads in BAM file.

Bin size used for generation of coverage tracks. The larger the bin size the smaller are the coverage tracks, however, the less precise is the signal. For single bp resolution set to 1.

Sample ID used for naming the output files.

Path to a tab-delimited file listing chromosome sizes in following fashion:\n \"chromosome_name<tab>total_number_of_bp\".\n For the most common UCSC genome build, you can find corresponding files at: https://github.com/CompEpigen/ATACseq_workflows/tree/master/chrom_sizes. Or you can generate them yourself using UCSC script fetchChromSizes (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes) in following fashion:\n \"fetchChromSizes hg38 > hg38.chrom.sizes\".\n If you are dealing with a non-UCSC build, you can generate such a file from a samtools index using:\n \"awk -v OFS='\t' {'print $1,$2'} hg38.fa.fai > hg38.chrom.sizes\".

Q-value cutoff used for peak calling by MACS2. The default is 0.05.

The effectively mappable genome size, please see: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html

List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. Specify as space-delimited string. Default: \"chrX chrY chrM\"