Index

Symbols | B | F | G

Symbols

--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
-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

B

bam2aln command line option
-b <file_path>, --bam=<file_path>
-f <file_path>, --fasta=<file_path>
-n <int>, --max-reads=<int>
-o <path>, --output=<path>
bam2cov command line option
--pdf
-1, --total_only
-b <file_path>, --fasta <file_path>
-f <file_path>, --fasta <file_path>
-o <path>, --output <path>
-r <int>, --resolution <int>
-t, --table
breseq command line option
--base-quality-cutoff=<int>
--max-rejected-polymorphisms-to-show <int>
--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
-r <file_path>, --reference <file_path>

F

fastq_utils command line option
-f <format>, --format=<format>
-l, --list-format
-n <int>, -n ALL, --num=<int>, --num=ALL

G

genomediff command line option
-o <file_path>, --output=<file_path>
-r <file_path>, --reference=<file_path>