Genomecomb moved to github on https://github.com/derijkp/genomecomb
with documentation on https://derijkp.github.io/genomecomb.
For up to date versions, go there. These pages only remain here for the data on the older scientific
application (or if someone really needs a long obsolete version of the software)
Reference
Format
cg subcommand ?options? ....
Description
This help page gives a (reference style) overview of all
genomecomb functions. For an introductory text to genomecomb and its
formats, use
cg help intro
All genomecombs functions are called using the cg command and a
subcommand. The available subcommands are listed on this page (in
categories) with a short description. To get further info on how to
use the subcommands and their parameters, use
cg help subcommand
or
cg subcommand -h
Options
The following options are generic and available for all
subcommands. They must however always preceed the subcommand specific
options.
- -v number (--verbose)
- Setting this to 1 or 2 (instead of the default 0) makes some
subcommands chattier about their progress. At the given number is
1, logging messages are shown (warnings, start of subtask, etc.) If
the number >= 2, progress counters are also shown (for commands
that support them)
- --stack 0/1
- When the program returns an error, by default only the error
message is shown, which is normally ok to show errors in input
format, etc. if --stack is set to 1, a full stack trace is shown on
error (which may be useful to solve errors caused by bugs in the
program)
Available subcommands
Process
- process_project
- process a sequencing project directory (projectdir), generating full analysis
information (variant calls, multicompar, reports, ...) starting
from raw sample data from various sources.
- process_multicompar
- process a sequencing project directory. This expects a
genomecomb directory with samples already processed and makes
annotated multicompar data
- process_reports
- Calculates a number of statistics on a sample in the reports
subdir
- process_sample
- Processes one sample directory (projectdir), generating full analysis
information (variant calls, multicompar, reports, ...) starting
from raw sample data that can come from various sources.
- project_addsample
- Add a sample directory to a project directory.
- renamesamples
- Converts the sample names in a file or entire directory to
other names.
Query
- select
- Command for very flexible selection, sorting and conversion
of tab separated files
- viz
- grahical vizualization of tsv files (even very large ones) as
table without loading everything into memory
- multiselect
- Command for using cg select on multiple files, and combine
the results
- groupby
- Group lines in a tsv file, based on 1 or more identical
fields
Analysis
- exportplink
- make a plink "Transposed fileset" from the genome
data
- homwes
- finds regions of homozygosity based on a variant file
- homwes_compare
- finds regions of homozygosity based on a variant file
Regions
- multireg
- Compare multiple regions files
- regselect
- select all regions or variants in region_file1 that overlap
with regions in region_file2
- covered
- Find number of bases covered by regions in a region file
- regcollapse
- Collapses overlapping regions in one (sorted) or more region
files
- regcommon
- list regions common between region_file1 and region_file2
- regextract
- Find regions with a minimum or maximum coverage in a bam,
bcol or tsv file.
- regjoin
- join regions in 1 or 2 regionfiles
- regsubtract
- subtract regions in region_file2 from region_file1
Annotation
- annotate
- Annotate a variant file with region, gene or variant data
- download_biograph
- download_biograph gene rank data from biograph.
- download_mart
- Download data from biomart
- geneannot2reg
- Creates a (region) annotation file based on a genelist with
annotations.
Validation
- genome_seq
- Returns sequences of regions in the genome (fasta file),
optionally masked for snps/repeats
- makeprimers
- Make sequencing primers for Sanger validation experiments
- makesequenom
- Make input files for designing sequenom validation
experiments
- primercheck
- check primer sets for multiple amplicons and snps
- validatesv
tsv
- cat
- Concatenate tab separated files and print on the standard
output (stripping headers of files other than the first).
- checktsv
- Checks the given tsv file for errors
- collapsealleles
- Convert a split variant file to unsplit by collapsing alleles
of the same variant into one line.
- graph
- Visualization of large tsv files as a scatter plot
- index
- make indices for a tsv file
- less
- view a (possibly compressed) file using the pager less.
- paste
- merge lines of tab separated files.
- split
- split a tab separated file in multiple tab separated files
based on the content of a (usually chromosome) field.
- tsvjoin
- join two tsv files based on common fields (must be sorted).
Conversion
- sam_clipamplicons
- Clip primers from aligned sequences in a sam file (by
changing bases to N and quality to 0) given a set of target
amplicons
- liftover
- Use liftover to convert a variant file from one build to
another
- liftregion
- Use liftover to convert a region file from one build to
another
- liftsample
- Use liftover to convert the files from a sample (variant,
region, ...) from one build to another
- liftchain2tsv
- Converts data in UCSC chain file format (for liftOver) to a
tsv (tab separated) format to be used in e.g. cg liftregion.
- correctvariants
- Complete or correct a variants file
- bamreorder
- Changes the order of the contigs/chromosomes in a bam file
Format Conversion
- bam2fastq
- Extracts reads from a bamfile into fastq. The actual
extraction is based on picard's SamToFastq or samtools bam2fq, but
the data is prepared first (ao. sorted by name to avoid the
problems caused by position sorted fq files)
- bam2reg
- Extract regions with a minimum coverage from a bam file.
- bcol
- several commands for managing bcol files
- bcol_get
- Get a list of values from a bcol file
- bcol_make
- Creates a bcol file
- bcol_table
- Outputs the data in a bcol file as
tab-separated
- bcol_update
- updates bcol file(s) in the old format to the new
- bed2tsv
- Converts data in bed format to tsv
format
- cg2sreg
- Extracts sequenced region data from a Complete Genomics
format file in tsv (tab separated, simple feature table) format.
The command will also sort the tsv appropriately.
- cg2tsv
- Converts data in Complete Genomics format to tsv (tab
separated, simple feature table) format. The command will also sort
the tsv appropriately. The cggenefile is optional. It contains the
CG gene annotations, which can be (best) left out as these
annotations (and more) can be done in genomecomb.
- clc2tsv
- Converts output from the clc bio assembly cell snp caller to
sft (simple feature table) format
- colvalue
- Converts data in tsv format from a long key-value format to a
wide column-value format
- convcgcnv
- Convert the Complete Genomics CNV files to the cg format
- convcgsv
- Convert the Complete Genomics SV files to the cg format
- csv2tsv
- Converts comma-separated value (csv) data to tab-sparated (tsv)
- gene2reg
- Extract gene elements from data in genepred-like format to a
(tab separated) region file.
- gff2tsv
- Converts data in gff format to gene sft (simple feature
table) format
- gtf2tsv
- Converts data in gtf format to gene sft (simple feature
table) format
- keyvalue
- Converts data in tsv format from wide format (data for each
sample in separate columns) to keyvalue format.
- long
- Converts data in tsv format from wide format (data for each
sample in separate columns) to long format (data for each sample in
separate lines)
- process_rtgsample
- Convert rtg data to cg format
- rtg2tsv
- Converts data in rtg format to sft (simple feature table)
format
- tsv2bed
- Converts data in tab-separated format (tsv) format to bed format. By default it will
create a minimal bed file by extracting chromosome,begin and end
from the input using the default fields.
- vcf2tsv
- Converts data in vcf format to genomecomb tab-separated
variant file (tsv). The command will also
sort the tsv appropriately.
- wide
- Converts data in tsv format from long format (data for each
sample in separate lines) to wide format (data for each sample in
separate columns)
Compare
- multicompar
- Compare multiple variant files
- multicompar_reannot
- Reannotate multicompar file
- pmulticompar
- Compare multiple variant files
Report
- coverage_report
- generates coverage report for region of interest A histo file
is generated at the location of the bam file
- depth_histo
- makes a histogram of the depth in the given bamfile,
subdivided in on- and oftarget regions
- hsmetrics
- Creates a hsmetrics file using picard CalculateHsMetrics
- predictgender
- predicts gender for a sample
Structural variants
- process_sv
- Do all steps on a Complete Genomics sample to generate
structural variant calls
- svmulticompar
- Compare multiple structural variant files
Compression
- bgzip
- Compresses files using bgzip
- job_update
- updates the logfile of a command using joboptions
- lz4
- Compresses files using lz4
- lz4ra
- decompresses part of a lz4 compressed file
- razip
- Compresses files using razip
- unzip
- Decompresses
- zcat
- pipe contents of one or more (potentially compressed) files
to stdout.
Dev
- help
- display help
- qsub
- submit a command to the cluster (grid engine).
- sh
- runs a shell in which genomecomb commands can be input and
executed interactively.
- source
- runs a script (Tcl) with all commands/extensions from
genomecomb available.
- tsvdiff
- compare tsv files
Tools
- cplinked
- create a copy of a directory where each file in it is a
softlink to the src.
- hardsync
- creates a hardlinked copy of a directory in another location
