Remove duplicates , ensuring only uniquely mapped reads are retained. #####%%%%% output "duplicates" are used in line8
{"action": "remove", "output": "duplicates", "temperature": [""]}
align the reads to the reference genome using your preferred aligner
{"action": "align", "output": "", "device": ["your preferred aligner"]}
If alignment quality is low, repeat the alignment process.
{"action": "repeat", "output": ""}
Use the BAM files , utilizing a virtual environment . #####%%%%% output "human samples" are used in line10
{"action": "use", "output": "human samples", "device": ["a virtual environment"], "reagent": ["BAM files", "duplicates"]}
For human samples, average on Alu repeats; for mouse samples, repeats. #####%%%%% output "Alu repeats" are not used
{"action": "repeat", "output": "Alu repeats", "reagent": ["human samples"]}
If the genome does not have built-in support, prepare the necessary regions, . #####%%%%% output "the necessary regions" are not used
{"action": "prepare", "output": "the necessary regions", "container": ["support"]}