Index

Symbols

--base-quality-cutoff=<int> breseq command line option --html gdtools-ANNOTATE command line option --max-rejected-polymorphisms-to-show <int> breseq command line option --plot-format=<plot_format> breseq 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 --require-complete-match breseq command line option

--required-match-length breseq command line option --resolution=<int> breseq command line option -1, --total-only breseq command line option -b <file_path>, --bam=<file_path> breseq command line option, [1] -f <file_path>, --fasta=<file_path> breseq command line option, [1] -f <output_format>, --format=<output_format> gdtools-APPLY command line option -n <int>, --max-reads=<int> breseq command line option -o <file_path>, --output=<file_path> gdtools-ANNOTATE command line option gdtools-APPLY command line option gdtools-INTERSECT command line option gdtools-SUBTRACT command line option -o <path>, --output=<path> breseq command line option, [1] -r <file_path>, --reference <file_path> breseq command line option -r <file_path>, --reference=<file_path> gdtools-ANNOTATE command line option gdtools-APPLY command line option -t, --table breseq command line option

B

breseq command line option --base-quality-cutoff=<int> --max-rejected-polymorphisms-to-show <int> --plot-format=<plot_format> --polymorphism-bias-p-value-cutoff <double> --polymorphism-coverage-both-strands <int> --polymorphism-frequency-cutoff <double> --polymorphism-log10-e-value-cutoff <float> --polymorphism-prediction --polymorphism-reject-homopolymer-length <int> --predict-polymorphisms --require-complete-match --required-match-length --resolution=<int> -1, --total-only -b <file_path>, --bam=<file_path>, [1] -f <file_path>, --fasta=<file_path>, [1] -n <int>, --max-reads=<int> -o <path>, --output=<path>, [1] -r <file_path>, --reference <file_path> -t, --table

G

gdtools-ANNOTATE command line option --html -o <file_path>, --output=<file_path> -r <file_path>, --reference=<file_path> gdtools-APPLY command line option -f <output_format>, --format=<output_format> -o <file_path>, --output=<file_path> -r <file_path>, --reference=<file_path>

gdtools-INTERSECT command line option -o <file_path>, --output=<file_path> gdtools-SUBTRACT command line option -o <file_path>, --output=<file_path>