- --base-quality-cutoff=<int>
- breseq command line option
- --max-rejected-polymorphisms-to-show <int>
- breseq command line option
- --pdf
- bam2cov command line option
- --polymorphism-bias-p-value-cutoff <double>
- breseq command line option
- --polymorphism-coverage-both-strands <int>
- breseq command line option
- --polymorphism-frequency-cutoff <double>
- breseq command line option
- --polymorphism-log10-e-value-cutoff <float>
- breseq command line option
- --polymorphism-prediction
- breseq command line option
- --polymorphism-reject-homopolymer-length <int>
- breseq command line option
- --predict-polymorphisms
- breseq command line option
- -1, --total_only
- bam2cov command line option
- -b <file_path>, --bam=<file_path>
- bam2aln command line option
- -b <file_path>, --fasta <file_path>
- bam2cov command line option
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- -f <file_path>, --fasta <file_path>
- bam2cov command line option
- -f <file_path>, --fasta=<file_path>
- bam2aln command line option
- -f <format>, --format=<format>
- fastq_utils command line option
- -l, --list-format
- fastq_utils command line option
- -n <int>, --max-reads=<int>
- bam2aln command line option
- -n <int>, -n ALL, --num=<int>, --num=ALL
- fastq_utils command line option
- -o <file_path>, --output=<file_path>
- genomediff command line option
- -o <path>, --output <path>
- bam2cov command line option
- -o <path>, --output=<path>
- bam2aln command line option
- -r <file_path>, --reference <file_path>
- breseq command line option
- -r <file_path>, --reference=<file_path>
- genomediff command line option
- -r <int>, --resolution <int>
- bam2cov command line option
- -t, --table
- bam2cov command line option
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