Manual
Documentation for Sandy version 0.20
Contents
Usage and option summary
General Syntax
Usage:
$ sandy [options]
$ sandy help <command>
$ sandy <command> [options] <FILEs>
where there are basically two commands for general help, two main commands
with their own inner options, tree database management commands, some
miscellaneous commands and a specific help command for each of the main
commands. See:
| Options | Description |
|---|---|
| -h, –help | brief help message |
| -u, –man | full documentation |
| Help commands: | |
| help | show application or command-specific help |
| man | show application or command-specific documentation |
| Misc commands: | |
| version | print the current version |
| citation | export citation in BibTeX format |
| Database commands: | |
| quality | manage quality profile database |
| expression | manage expression-matrix database |
| variation | manage structural variation database |
| Main commands: | |
| genome | simulate genome sequencing |
| transcriptome | simulate transcriptome sequencing |
Some examples:
- If you want to see a brief help for the
expressioncommand, type either of the commands bellow:$ sandy help expressionor
$ sandy expression -h - To view the version of Sandy in use, just type:
$ sandy version - And, to take a BibTeX entry to cite Sandy in your work, type:
$ sandy citation
Main Commands
Command genome
Use it to generate simulated FASTq-files from a given FASTA-file.
The genome command sets these default options for a genome sequencing simulation:
- The strand is randomly chosen;
- The number of reads is calculated by the coverage;
- The chromosomes are raffled following a weighted raffle with the sequence length as the bias;
Usage:
$ sandy genome [options] <FILEs>
whose options’ exhaustive list can be consulted by sandy genome -h or
even sandy help genome commands.
At least one fasta-file must be given as the <FILEs> term. The results
will be one or two fastq-files, depending on the sequencing-type option,
-t, for single-ended or paired-ended reads, and an additional reads-count
file.
| Options | Description |
|---|---|
| -h, –help | brief help message |
| -u, –man | full documentation |
| -v, –verbose | print log messages |
| -p, –prefix | prefix output [default:”out”] |
| -o, –output-dir | output directory [default:”.”] |
| -O, –output-format | bam, sam, fastq.gz, fastq [default:”fastq.gz”] |
| -1, –join-paired-ends | merge R1 and R2 outputs in one file |
| -x, –compression-level | speed compression: “1” - compress faster, “9” - compress better [default:”6”; Integer] |
| -i, –append-id | append to the defined template id [Format] |
| -I, –id | overlap the default template id [Format] |
| -j, –jobs | number of jobs [default:”1”; Integer] |
| -s, –seed | set the seed of the base generator [default:”time()”; Integer] |
| -c, –coverage | fastq-file coverage [default:”8”, Number] |
| -t, –sequencing-type | single-end or paired-end reads [default:”paired-end”] |
| -q, –quality-profile | sequencing system profiles from quality database [default:”poisson”] |
| -e, –sequencing-error | sequencing error rate [default:”0.005”; Number] |
| -r, –read-size | the read size [default:”100”; Integer] the quality_profile from database overrides this value |
| -M, –fragment-mean | the fragment mean size for paired-end reads [default:”300”; Integer] |
| -D, –fragment-stdd | the fragment standard deviation size for paired-end reads [default:”50”; Integer] |
| -a, –structural-variation | a list of structural variation entries from variation database. This option may be passed multiple times [default:”none”] |
| -A, –structural-variation-regex | a list of perl-like regex to match structural variation entries in variation database. This option may be passed multiple times [default:”none”] |
Some examples:
- These two commands, with equal effects, will produce two FASTq-files
(sequencing-type default is “paired-end”), both with a coverage of 20x
(coverage default is 8), and a plain-text reads-count file in a tab separated
fashion.
$ sandy genome --verbose --sequencing-type=paired-end --coverage=20 hg38.fa 2> sim.logor
$ sandy genome -v -t paired-end -c 20 hg38.fa 2> sim.log - For reproducibility, you can set an integer seed for the random raffles
with the
-soption (seed default is environmenttime()value), for example:$ sandy genome -s 1220 my_fasta.fa - To simulate reads from a ready registered database with a specific quality
profile other than default’s one, type, for example:
$ sandy genome --quality-profile=hiseq_101 hg19.faSee the quality profile section to know how you can register a new profile on the database. Note: If you use the option
-v, by default, the log messages will be directed to the standard error so, in the example above, it was redirected to a file. Without the-voption, only errors messages will be printed. - The sequence identifier is the first and third line of a FASTq entry
beginning with a @ token, for a read identifier, and a +,
for a quality identifier.
Sandy has the capacity to customize it, with a format string passed by
the user. This format is a combination of literal and escaped characters,
in a similar fashion used in C programming language’s
printffunction. For example, let’s simulate a paired-end sequencing and put into it’s identifier the read length, read position and mate position:$ sandy genome -s 123 --id="%i.%U read=%c:%t-%n mate=%c:%T-%N length=%r" hg38.faIn this case, results would be:
$ sandy genome -s 123 --id="%i.%U read=%c:%t-%n mate=%c:%T-%N length=%r" hg38.fa ==> Into R1 @SR.1 read=chr6:979-880 mate=chr6:736-835 length=100 ... ==> Into R2 @SR.1 read=chr6:736-835 mate=chr6:979-880 length=100 ... - To change the sequencing quality profile, use the
-qoption and a string value (quality-profile default is “hiseq”):$ sandy genome -q hiseq2 my_fasta_file.fa - You can set the size of the reads with the
-roption and an integer number (reads-size default is 101):$ sandy genome -r 151 my_fasta_file.fa - You can set the mean size of a fragment in a paired-end sequencing with
the
-Moption and an integer number (default is 300):$ sandy genome -M 300 my_fasta_file.fa - Also, you can also set the standard deviation of the size of a fragment in
a paired-end sequencing with the
-Doption and an integer number (default is 50):$ sandy genome -D 30 my_fasta_file.fa - The options above are the most frequently used ones for the
genomecommand, but many more can be found in the Sandy’s documentation, with:$ sandy genome --man
Command transcriptome
Use it to generate simulated FASTq files from a given FASTA file,
according to an expression profile matrix file.
The transcriptome command sets these default options for a transcriptome
sequencing simulation as well:
- Choose the Minus strand;
- The number of reads is directly passed;
- The genes/transcripts are raffled following the expression matrix;
Usage:
$ sandy transcriptome [options] <FILEs>
whose options’ exhaustive list can be consulted by sandy transcriptome -h or
even sandy help transcriptome commands.
| Options | Description |
|---|---|
| -h, –help | brief help message |
| -u, –man | full documentation |
| -v, –verbose | print log messages |
| -p, –prefix | prefix output [default:”out”] |
| -o, –output-dir | output directory [default:”.”] |
| -O, –output-format | bam, sam, fastq.gz, fastq [default:”fastq.gz”] |
| -1, –join-paired-ends | merge R1 and R2 outputs in one file |
| -x, –compression-level | speed compression: “1” - compress faster, “9” - compress better [default:”6”; Integer] |
| -i, –append-id | append to the defined template id [Format] |
| -I, –id | overlap the default template id [Format] |
| -j, –jobs | number of jobs [default:”1”; Integer] |
| -z, –gzip | compress output file |
| -s, –seed | set the seed of the base generator [default:”time()”; Integer] |
| -n, –number-of-reads | set the number of reads [default:”1000000”, Integer] |
| -t, –sequencing-type | single-end or paired-end reads [default:”paired-end”] |
| -q, –quality-profile | illumina sequencing system profiles [default:”hiseq”] |
| -e, –sequencing-error | sequencing error rate [default:”0.005”; Number] |
| -r, –read-size | the read size [default:”101”; Integer] |
| -M, –fragment-mean | the fragment mean size for paired-end reads [default:”300”; Integer] |
| -D, –fragment-stdd | the fragment standard deviation size for paired-end reads [default:”50”; Integer] |
Some examples:
- The command:
$ sandy transcriptome --verbose --number-of-reads=1000000 --expression-matrix=brain_cortex gencode_pc_v26.fa.gzor, equivalently
$ sandy transcriptome -v -n 1000000 -f brain_cortex gencode_pc_v26.fa.gzwill both generate a FASTq file with 1000000 reads from the gencode_pc_v26.fa.gz file and a plain text file with the raw counts of the reads per gene, according to the expression matrix provided by the brain_cortex entry already registered in the database.
- To demonstrate some other features, think about the sequencing error rate
that can be set between 0 and 1. By default, Sandy set this value to
0.005, which means 1 error every 200 bases. To set it to another value,
try:
$ sandy transcriptome -f liver --sequencing-error=0.001 genome_pc_v26.fa.gz - For reproducibility, the user can set the
seedoption and guarantee the reliability of all the raffles in a later simulation.$ sandy transcriptome -q hiseq_101 --seed=123 transcripts.fa - To have an idea of Sandy’s plurality, look to how overwhelming the number
of choices could be:
$ sandy transcriptome \ --expression-matrix=pancreas \ --quality-profile=hiseq_101 \ --sequencing-type=paired-end \ --fragment-mean=350 \ --fragment-stdd=100 \ --prefix=pancreas_sim \ --output-dir=sim_dir \ --id="%i.%U read=%c:%t-%n mate=%c:%T-%N length=%r" \ --verbose \ --seed=123 \ --jobs=30 \ --no-gzip \ gencode_pc_v26.fa.gz
A note on parallelism: To increase the processing speed, the simulation can run in parallel, splitting the task among jobs. For example, type:
$ sandy transcriptome --jobs 15 gencode_lnc.fa.gz
and Sandy will allocate 15 jobs. This feature works for the genome and
the transcriptome commands as well.
Database Commands
Command quality
Use it to manage your quality profile database. You can add or remove your own expression profiles in the builtin database and turn your simulations more realistic based on real experimental data. Or you can even clean it up to restore the vendor’s original entries state. By default, Sandy uses a Poisson distribution when compiling the quality entries, but like many other features, this behavior can be overridden by the user.
Usage:
$ sandy quality
$ sandy quality [options]
$ sandy quality <sub-command>
whose options’ exhaustive list can be consulted by sandy quality -h or
even sandy help quality commands.
| Options | Description |
|---|---|
| -h, –help | brief help message |
| -u, –man | full documentation |
| Sub-Commands | |
| add | add a new quality profile to database |
| dump | dump a quality-profile from database |
| remove | remove an user quality profile from database |
| restore | restore the database |
Some examples:
- To list the quality profiles already registered in the builtin database, you
can simply type:
$ sandy qualityand all entries will be shown:
.--------------------------------------------------------------------. | quality profile | size | source | provider | date | +-----------------+------+-------------------+----------+------------+ | hiseq_101 | 101 | 1000 genome | vendor | 2018-05-05 | | hiseq_150 | 150 | SRA ID=SRR5805510 | vendor | 2018-05-05 | | hiseq_51 | 51 | SRA ID=SRR3185389 | vendor | 2018-05-05 | | hiseq_76 | 76 | SRA ID=SRR3355336 | vendor | 2018-05-05 | | miseq_150 | 150 | SRA ID=SRR6876696 | vendor | 2018-05-05 | | miseq_301 | 301 | SRA ID=SRR7089434 | vendor | 2018-05-05 | | nextseq_51 | 51 | SRA ID=SRR6131534 | vendor | 2018-05-05 | | nextseq_85 | 85 | SRA ID=SRR5445416 | vendor | 2018-05-05 | '-----------------+------+-------------------+----------+------------' - To register a new probabilistic quality profile called, for example,
‘my_profile.txt’ to be used in the simulation of your FASTA-file.
You can use the
addsub-command, typing:$ sandy quality add my_profile.txtThis quality profile can be either a FASTq file or a plain text file in a tab separated fashion (quality profile default density function is Poisson).
Note: Before the new entry can appear in the database’s list, the new profile needs to be validated, and if it can’t, an error message will be show. Sandy prevents you before overwrite an existing entry. - To use your recently inserted quality profile over a given FASTA file
to simulate a transcriptomic data, use the
-qoption with the id you registered:$ sandy genome -q my_profile my_fasta.fa - Sometimes you will need to update or delete some quality profile entry
(
my_profile.txtfor example) in the database. In this situation, you can remove some actual entry and register a newer one, like this:$ sandy quality remove my_profile.txtSandy will refuse to remove any vendor’s original entry from the database.
- And, there could be times when you would want to reset all the database to
its original state. It’s a very simple command:
$ sandy quality restoreNote that this is a dangerous command and Sandy will warn you about it before make the restoration in fact.
Note: Sandy already comes with one quality profile based on the Poisson probabilistic curve, as described by the literature (illumina, 2018).
Command expression
The expression command is used to verify and update the expression matrix
database. In a transcriptome sequencing simulation, the user
must provide an expression matrix indexed into this database. Sandy
already comes with 52 different tissues from the GTEx project, but the
user has the freedom to include his own data as well, or even clean it up
to restore the vendor’s original entries state.
Usage:
$ sandy expression
$ sandy expression [options]
$ sandy expression <sub-command>
whose options’ and sub-commands’ exhaustive list can be consulted by
sandy expression -h or even sandy help expression commands.
| Options | Description |
|---|---|
| -h, –help | brief help message |
| -u, –man | full documentation |
| Sub-Commands | |
| add | add a new expression-matrix to database |
| dump | dump an expression-matrix from database |
| remove | remove an user expression-matrix from database |
| restore | restore the database |
Some examples:
- To list the expression matrices already registered in the builtin database,
you can simply type:
$ sandy expressionand all registered entries will be shown:
.----------------------------------------------------------------------------------. | expression-matrix | source | provider | date | +-------------------------------------+--------------------+----------+------------+ | adipose_subcutaneous | Xena GTEx Kallisto | vendor | 2018-05-05 | | adipose_visceral | Xena GTEx Kallisto | vendor | 2018-05-05 | | adrenal_gland | Xena GTEx Kallisto | vendor | 2018-05-05 | | artery_aorta | Xena GTEx Kallisto | vendor | 2018-05-05 | | artery_coronary | Xena GTEx Kallisto | vendor | 2018-05-05 | | artery_tibial | Xena GTEx Kallisto | vendor | 2018-05-05 | | bladder | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_amygdala | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_anterior_cingulate_cortex | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_caudate | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_cerebellar_hemisphere | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_cerebellum | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_cortex | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_frontal_cortex | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_hippocampus | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_hypothalamus | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_nucleus_accumbens | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_putamen | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_spinal_cord | Xena GTEx Kallisto | vendor | 2018-05-05 | | brain_substantia_nigra | Xena GTEx Kallisto | vendor | 2018-05-05 | | breast_mammary_tissue | Xena GTEx Kallisto | vendor | 2018-05-05 | | cells_ebv_transformed_lymphocytes | Xena GTEx Kallisto | vendor | 2018-05-05 | | cells_leukemia_cell_line | Xena GTEx Kallisto | vendor | 2018-05-05 | | cells_transformed_fibroblasts | Xena GTEx Kallisto | vendor | 2018-05-05 | | cervix_ectocervix | Xena GTEx Kallisto | vendor | 2018-05-05 | | cervix_endocervix | Xena GTEx Kallisto | vendor | 2018-05-05 | | colon_sigmoid | Xena GTEx Kallisto | vendor | 2018-05-05 | | colon_transverse | Xena GTEx Kallisto | vendor | 2018-05-05 | | esophagus_gastroesophageal_junction | Xena GTEx Kallisto | vendor | 2018-05-05 | | esophagus_mucosa | Xena GTEx Kallisto | vendor | 2018-05-05 | | esophagus_muscularis | Xena GTEx Kallisto | vendor | 2018-05-05 | | fallopian_tube | Xena GTEx Kallisto | vendor | 2018-05-05 | | heart_atrial_appendage | Xena GTEx Kallisto | vendor | 2018-05-05 | | heart_left_ventricle | Xena GTEx Kallisto | vendor | 2018-05-05 | | kidney_cortex | Xena GTEx Kallisto | vendor | 2018-05-05 | | liver | Xena GTEx Kallisto | vendor | 2018-05-05 | | lung | Xena GTEx Kallisto | vendor | 2018-05-05 | | minor_salivary_gland | Xena GTEx Kallisto | vendor | 2018-05-05 | | muscle_skeletal | Xena GTEx Kallisto | vendor | 2018-05-05 | | nerve_tibial | Xena GTEx Kallisto | vendor | 2018-05-05 | | ovary | Xena GTEx Kallisto | vendor | 2018-05-05 | | pancreas | Xena GTEx Kallisto | vendor | 2018-05-05 | | pituitary | Xena GTEx Kallisto | vendor | 2018-05-05 | | prostate | Xena GTEx Kallisto | vendor | 2018-05-05 | | skin_not_sun_exposed | Xena GTEx Kallisto | vendor | 2018-05-05 | | skin_sun_exposed | Xena GTEx Kallisto | vendor | 2018-05-05 | | small_intestine_terminal_ileum | Xena GTEx Kallisto | vendor | 2018-05-05 | | spleen | Xena GTEx Kallisto | vendor | 2018-05-05 | | stomach | Xena GTEx Kallisto | vendor | 2018-05-05 | | testis | Xena GTEx Kallisto | vendor | 2018-05-05 | | thyroid | Xena GTEx Kallisto | vendor | 2018-05-05 | | uterus | Xena GTEx Kallisto | vendor | 2018-05-05 | | vagina | Xena GTEx Kallisto | vendor | 2018-05-05 | | whole_blood | Xena GTEx Kallisto | vendor | 2018-05-05 | '-------------------------------------+--------------------+----------+------------' - But, suppose you want to register a new expression matrix file called
my_expression.txtto simulate your FASTA-file according to its experimentally annotated data. In this case, the sub-commandaddwould solve your problem:$ sandy expression add my_expression.txtNote that, before the new entry can appear in the database’s list, the new matrix file needs to be validated, and if it can’t, an error message will be show. Sandy prevents you to overwrite an existing entry.
- So, to use your recently added expression matrix in a transcriptome
simulation, use the
-foption of thetranscriptomecommand:$ sandy expression -f my_expression.txt my_fasta.fa - Sometimes you will need to update or delete some expression-matrix entry
(‘my_expression.txt’, for example) in the database. In this situation, you can
remove the actual entry and register a newer one, like this:
$ sandy expression remove my_expression.txtSandy will refuse to remove any vendor’s original entry from the database.
- Finally, there could be times when you would want to reset all the database to
its original state. It’s a very simple command:
$ sandy expression restoreNote that this is a dangerous command and Sandy will warn you about it before make the restoration in fact.
Command variation
Usage:
$ sandy variation
$ sandy variation [options]
$ sandy variation <sub-command>
whose options’ and sub-commands’ exhaustive list can be consulted by
sandy variation -h or even sandy help variation commands.
| Options | Description |
|---|---|
| -h, –help | brief help message |
| -u, –man | full documentation |
| Sub-Commands: | |
| add | add a new structural variation to database |
| dump | dump structural variation from database |
| remove | remove an user structural variation from database |
| restore | restore the database |
Some Examples:
- To show all variations entries in the database, type:
$ sandy variationsand all entries for variations will be shown:
.---------------------------------------------------------------------------------------------. | structural variation | source | provider | date | +---------------------------+-----------------------------------------+----------+------------+ | NA12878_hg38_chr1 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr10 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr11 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr12 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr13 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr14 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr15 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr16 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr17 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr18 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr19 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr2 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr20 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr21 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr22 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr3 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr4 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr5 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr6 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr7 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr8 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chr9 | IGSR - Phase 3 | vendor | 2018-07-06 | | NA12878_hg38_chrX | IGSR - Phase 3 | vendor | 2018-07-06 | | RTC_sim | HSL Bioinfo | user | 2018-07-23 | | fusion_hg38_BCR-ABL1 | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_CCDC6-RET | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_EML4-ALK | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_EWSR1-ERG | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_EWSR1-FLI1 | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_KIAA1549-BRAF | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_KMT2A-AFF1 | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_NCOA4-RET | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_NPM1-ALK | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | | fusion_hg38_TMPRSS2-ERG | COSMIC - The 10 most cited gene fusions | vendor | 2018-07-06 | '---------------------------+-----------------------------------------+----------+------------' - To increase the database with your own data, use the
addsub-command, like this:sandy variation add my_vatiations.txtNote that, before the new entry can appear in the database’s list, the new variation’s file needs to be validated, and if it can’t, an error message will be show. Sandy will prevent you to overwrite any existing entry, and Sandy require these variations files to be in a GTF like format, specifying coordinates on a reference genome with one variation per line (INDELs, SNVs and gene fusions).
- Now, to use your recently added variations specifications in a genomic
project, you can use the
-aoption with the id you registered for your file:sandy genome -a my_vatiations.txt hg38.fa - You can remove no-vendors entries from database as well:
sandy variation remove my_vatiations.txtNote that you can’t remove any vendor’s entry.
- Also, to reset all your variation entries to the original state (only with
the vendor’s data), use the
restoresub-command.sandy variation restore - Finally, if you want to simulate a reference genome with a high coverage
(ex. 50x) and insert some variations in it (maybe to obtain a positive control
for some other algorithm you’re using), try this:
sandy genome -c 50 -a NA12878_hg38_chrX hg38.faIn this example, you’ve simulated reads for the whole genome, but the variations are only in the X chromosome of the NA12878 individual in Sandy’s database. An even better way to insert variations to your simulations is to use a regular expression to search the entire database, like this:
sandy genome -c 50 -A NA12878* -a fusion_hg38_BCR-ABL1 hg38.faThis way you take all entries that match NA12878 variations and additionally introduce a well studied gene fusion fusion_hg38_BCR-ABL1.
See our case study to find out how to construct a complex genome with on demand variations in it.
Miscellaneous Commands
Command version
Sandy project is made in a rolling release way, so you can easily find the version number you’re using:
sandy version
Command citation
If Sandy was somehow useful, please cite its authors. With the citation
command, you can obtain a correct BibTeX entry and/or DOI number for the
version of Sandy you’re using:
sandy citation
Help Commands
Usage: To get a simple general help, you can type any of these commands:
$ sandy --help
or for short
$ sandy -h
or simply call it without any arguments.
$ sandy
But, if you need a more comprehensive explanation, you can invoke Sandy’s manual:
$ sandy --man
or for short
$ sandy -u
For help about specific commands, its options and inputs, type:
$ sandy help <command>
or
$ sandy <command> -h
And you can always get help by consulting Sandy’s manuals in your system’s
builtin documentations with man sandy or info sandy commands.