Parameters¶
Complete option reference for every ReSeq2 command. Select a tab to view the parameters for a specific command.
General
| Parameter | Default | Description |
|---|---|---|
-h --help |
Prints help information and exits | |
-j --threads |
0 | Number of threads used (0=auto) |
--verbosity |
4 | Sets the level of verbosity (4=everything, 0=nothing) |
--version |
Prints version info and exits |
Stats
| Parameter | Default | Description |
|---|---|---|
--adapterFile |
(AutoDetect) | Fasta file with adapter sequences |
--adapterMatrix |
(AutoDetect) | 0/1 matrix with valid adapter pairing (first read in rows, second read in columns) |
-b --bamIn |
None | Position sorted bam/sam file with reads mapped to --refIn |
--binSizeBiasFit |
100000000 | Reference sequences larger than this are split for bias fitting to limit memory consumption |
--maxFragLen |
2000 | Maximum fragment length to include pairs into statistics |
--minMapQ |
10 | Minimum mapping quality to include pairs into statistics |
--noBias |
Do not perform bias fit. Results in uniform coverage if simulated from | |
--noTiles |
Ignore tiles for the statistics [default] | |
-r --refIn |
None | Reference sequences in fasta format (gz and bz2 supported) |
--statsOnly |
Only generate the statistics | |
-s --statsIn |
None | Skips statistics generation and reads directly from stats file |
-S --statsOut |
--bamIn.reseq |
Stores the real data statistics for reuse in given file |
--tiles |
Use tiles for the statistics | |
-v --vcfIn |
None | Ignore all positions with a listed variant for stats generation |
--textFormat |
Write profile files in portable text format instead of compressed binary | |
--bothFormats |
Write profiles in both binary and text formats (alternate gets .text or .bin suffix) |
Probabilities
| Parameter | Default | Description |
|---|---|---|
--ipfIterations |
200 | Maximum number of iterations for iterative proportional fitting |
--ipfPrecision |
5 | Iterative proportional fitting procedure stops after reaching this precision (%) |
-p --probabilitiesIn |
--statsIn.ipf |
Loads last estimated probabilities and continues from there if precision is not met |
-P --probabilitiesOut |
--probabilitiesIn |
Stores the probabilities estimated by iterative proportional fitting |
--stopAfterEstimation |
Stop after estimating the probabilities |
Simulation
| Parameter | Default | Description |
|---|---|---|
-1 --firstReadsOut |
reseq-R1.fq | Writes the simulated first reads into this file |
-2 --secondReadsOut |
reseq-R2.fq | Writes the simulated second reads into this file |
-c --coverage |
0 | Approximate average read depth simulated (0 = Corrected original coverage) |
--errorMutliplier |
1.0 | Divides the original probability of correct base calls (no substitution error) by this value and renormalizes |
--methylation |
Extended bed graph file specifying methylation for regions. Multiple score columns for individual alleles are possible, but must match with vcfSim. C->T conversions for 1-specified value in region. | |
--noInDelErrors |
Simulate reads without InDel errors | |
--noSubstitutionErrors |
Simulate reads without substitution errors | |
--numReads |
0 | Approximate number of read pairs simulated (0 = Use --coverage) |
--readSysError |
None | Read systematic errors from file in fastq format (seq=dominant error, qual=error percentage) |
--recordBaseIdentifier |
ReseqRead | Base identifier for the simulated fastq records, followed by a count and other information about the read |
--refBias |
keep/no | Way to select the reference biases for simulation (keep [from refIn] / no [biases] / draw [with replacement from original biases] / file) |
--refBiasFile |
None | File to read reference biases from: one sequence per line (identifier bias) |
-R --refSim |
--refIn |
Reference sequences in fasta format to simulate from |
--seed |
None | Seed used for simulation; if none is given a random seed will be used |
-V --vcfSim |
None | Defines genotypes to simulate alleles or populations |
--writeSysError |
None | Write the randomly drawn systematic errors to file in fastq format (seq=dominant error, qual=error percentage) |
General
| Parameter | Default | Description |
|---|---|---|
-h --help |
Prints help information and exits | |
-j --threads |
0 | Number of threads used (0=auto) |
--verbosity |
4 | Sets the level of verbosity (4=everything, 0=nothing) |
--version |
Prints version info and exits |
queryProfile
| Parameter | Default | Description |
|---|---|---|
--fragLenBias |
None | Output fragment length bias to file (tsv format; - for stdout) |
--maxLenDeletion |
None | Output lengths of longest detected deletion to stdout |
--maxReadLength |
None | Output lengths of longest detected read to stdout |
-r --ref |
None | Reference sequences in fasta format (gz and bz2 supported) |
--refSeqBias |
None | Output reference sequence bias to file (tsv format; - for stdout) |
-s --stats |
None | Reseq statistics file to extract reference sequence bias |
General
| Parameter | Default | Description |
|---|---|---|
-h --help |
Prints help information and exits | |
-j --threads |
0 | Number of threads used (0=auto) |
--verbosity |
4 | Sets the level of verbosity (4=everything, 0=nothing) |
--version |
Prints version info and exits |
replaceN
| Parameter | Default | Description |
|---|---|---|
-r --refIn |
None | Reference sequences in fasta format (gz and bz2 supported) |
-R --refSim |
None | File to where reference sequences in fasta format with Ns randomly replaced should be written |
--seed |
None | Seed used for replacing N; if none is given a random seed will be used |
General
| Parameter | Default | Description |
|---|---|---|
-h --help |
Prints help information and exits | |
-j --threads |
0 | Number of threads used (0=auto) |
--verbosity |
4 | Sets the level of verbosity (4=everything, 0=nothing) |
--version |
Prints version info and exits |
seqToIllumina
| Parameter | Default | Description |
|---|---|---|
--errorMutliplier |
1.0 | Divides the original probability of correct base calls (no substitution error) by this value and renormalizes |
-i --input |
stdin |
Input file (fasta format, gz and bz2 supported) |
--ipfIterations |
200 | Maximum number of iterations for iterative proportional fitting |
--ipfPrecision |
5 | Iterative proportional fitting procedure stops after reaching this precision (%) |
--noInDelErrors |
Simulate reads without InDel errors | |
--noSubstitutionErrors |
Simulate reads without substitution errors | |
-o --output |
stdout |
Output file (fastq format, gz and bz2 supported) |
-p --probabilitiesIn |
--statsIn.ipf |
Loads last estimated probabilities and continues from there if precision is not met |
-P --probabilitiesOut |
--probabilitiesIn |
Stores the probabilities estimated by iterative proportional fitting |
--seed |
None | Seed used for simulation; if none is given a random seed will be used |
-s --statsIn |
None | Profile file that contains the statistics used for simulation |
--textFormat |
Write profile files in portable text format instead of compressed binary | |
--bothFormats |
Write profiles in both binary and text formats (alternate gets .text or .bin suffix) |
General
| Parameter | Default | Description |
|---|---|---|
-h --help |
Prints help information and exits | |
-j --threads |
0 | Number of threads used (0=auto) |
--verbosity |
4 | Sets the level of verbosity (4=everything, 0=nothing) |
--version |
Prints version info and exits |
convertProfile
| Parameter | Default | Description |
|---|---|---|
-s --statsIn |
None | Input stats file (.reseq) |
-o --statsOut |
Overwrites input | Output stats file |
-p --probsIn |
None | Input probabilities file (.reseq.ipf) |
-P --probsOut |
Overwrites input | Output probabilities file |
--textFormat |
Write in portable text format (default: compressed binary) |