cgatools version 1.8.0 build 1
usage: cgatools COMMAND [ options ] [ positionalArgs ]
For help on a particular command CMD, try "cgatools help CMD".
Available commands:
help Prints help information.
man Prints the cgatools reference manual.
fasta2crr Converts fasta reference files to the crr format.
crr2fasta Converts a crr reference file to the fasta format.
listcrr Lists chromosomes, contigs, or ambiguous sequences of a
crr file.
decodecrr Prints the reference sequence for a given reference
range.
snpdiff Compares snp calls to a Complete Genomics variant file.
calldiff Compares two Complete Genomics variant files.
listvariants Lists the variants present in a variant file.
testvariants Tests variant files for presence of variants.
evidence2sam Converts CGI variant evidence data into SAM format.
join Joins two tab-delimited files based on equal fields or
overlapping regions.
junctiondiff Reports difference between junction calls of Complete
Genomics junctions files.
junctions2events Groups and annotates junction calls by event type.
generatemastervar Converts a variation file to a one-line-per-locus
format.
varfilter Copies input var file or masterVar file to output,
applying specified filters.
mkvcf Converts var file(s) or masterVar file(s) to VCF.
-------------------------------------------------------------------------------
COMMAND NAME
help - Prints help information.
OPTIONS
-h [ --help ]
Print this help message.
--command arg
The command to describe.
--format arg (=text)
The format of the output stream (text or html).
--output arg (=STDOUT)
The output file (may be omitted for stdout).
-------------------------------------------------------------------------------
COMMAND NAME
man - Prints the cgatools reference manual.
OPTIONS
-h [ --help ]
Print this help message.
--output arg (=STDOUT)
The output file (may be omitted for stdout).
--format arg (=text)
The format of the output stream (text or html).
-------------------------------------------------------------------------------
COMMAND NAME
fasta2crr - Converts fasta reference files to the crr format.
OPTIONS
-h [ --help ]
Print this help message.
--input arg
The input fasta files (may be passed in as arguments at the end of the
command, or omitted for stdin). Take care to specify the fasta files in
chromosome order; ordering is important. To work with human Complete
Genomics data, the chromosome order should be chr1...chr22, chrX, chrY,
chrM.
--output arg
The output crr file.
--circular arg
A comma-separated list of circular chromosome names. If ommitted,
defaults to chrM.
-------------------------------------------------------------------------------
COMMAND NAME
crr2fasta - Converts a crr reference file to the fasta format.
OPTIONS
-h [ --help ]
Print this help message.
--input arg
The input crr file (may be passed in as argument at the end of the
command).
--output arg (=STDOUT)
The output fasta file (may be omitted for stdout).
--line-width arg (=50)
The maximum width of a line of sequence.
-------------------------------------------------------------------------------
COMMAND NAME
listcrr - Lists chromosomes, contigs, or ambiguous sequences of a crr file.
DESCRIPTION
For mode=chromosome, prints a space-separated table describing each
chromosome within the reference. The columns are defined as follows:
ChromosomeId A numeric identifier for the chromosome.
Chromosome The name of the chromosome.
Length The length in bases of the chromosome.
Circular Boolean indicating if the chromosome is circular.
Md5 Md5 of the string containing the upper case IUPAC code for
each base in the chromosome (spaces and dashes are
omitted).
For mode=contig, prints a space-separated table describing each gap and
each contig within the reference. Here, a gap between contigs is defined as
any stretch of min-contig-gap-length or more no-called reference bases (N
character). The columns are defined as follows:
ChromosomeId A numeric identifier for the chromosome.
Chromosome The name of the chromosome.
Type Either CONTIG or GAP.
Offset The 0-based offset of the start of the contig or gap
within the chromosome.
Length The length in bases of the contig or gap.
For mode=ambiguity, prints a space-separated table describing each run of
ambiguity codes within the reference. The columns are defined as follows:
ChromosomeId A numeric identifier for the chromosome.
Chromosome The name of the chromosome.
Code The IUPAC code for the region.
Offset The 0-based offset of the run of ambiguity codes in the
chromosome.
Length The length in bases of the run of ambiguity codes.
OPTIONS
-h [ --help ]
Print this help message.
--reference arg
The reference crr file (may be passed in as argument at the end of the
command).
--output arg (=STDOUT)
The output file (may be omitted for stdout).
--mode arg (=chromosome)
One of chromosome, contig, or ambiguity.
--min-contig-gap-length arg (=50)
Minimum length of gap between reference contigs, for mode=contig.
-------------------------------------------------------------------------------
COMMAND NAME
decodecrr - Prints the reference sequence for a given reference range.
OPTIONS
-h [ --help ]
Print this help message.
--reference arg
The reference crr file (may be passed in as argument at the end of the
command).
--output arg (=STDOUT)
The output file (may be omitted for stdout).
--range arg
The range of bases to print (chr,begin,end or chr:begin-end).
-------------------------------------------------------------------------------
COMMAND NAME
snpdiff - Compares snp calls to a Complete Genomics variant file.
DESCRIPTION
Compares the snp calls in the "genotypes" file to the calls in a Complete
Genomics variant file. The genotypes file is a tab-delimited file with at
least the following columns (additional columns may be given):
Chromosome (Required) The name of the chromosome.
Offset0Based (Required) The 0-based offset in the chromosome.
GenotypesStrand (Optional) The strand of the calls in the Genotypes
column (+ or -, defaults to +).
Genotypes (Optional) The calls, one per allele. The following
calls are recognized:
A,C,G,T A called base.
N A no-call.
- A deleted base.
. A non-snp variation.
The output is a tab-delimited file consisting of the columns of the
original genotypes file, plus the following additional columns:
Reference The reference base at the given position.
VariantFile The calls made by the variant file, one per allele.
The character codes are the same as is described for
the Genotypes column.
DiscordantAlleles (Only if Genotypes is present) The number of
Genotypes alleles that are discordant with calls in
the VariantFile. If the VariantFile is described as
haploid at the given position but the Genotypes is
diploid, then each genotype allele is compared
against the haploid call of the VariantFile.
NoCallAlleles (Only if Genotypes is present) The number of
Genotypes alleles that were no-called by the
VariantFile. If the VariantFile is described as
haploid at the given position but the Genotypes is
diploid, then a VariantFile no-call is counted twice.
The verbose output is a tab-delimited file consisting of the columns of the
original genotypes file, plus the following additional columns:
Reference The reference base at the given position.
VariantFile The call made by the variant file for one allele (there is
a line in this file for each allele). The character codes
are the same as is described for the Genotypes column.
[CALLS] The rest of the columns are pasted in from the VariantFile,
describing the variant file line used to make the call.
The stats output is a comma-separated file with several tables describing
the results of the snp comparison, for each diploid genotype. The tables
all describe the comparison result (column headers) versus the genotype
classification (row labels) in different ways. The "Locus classification"
tables have the most detailed match classifications, while the "Locus
concordance" tables roll these match classifications up into "discordance"
and "no-call". A locus is considered discordant if it is discordant for
either allele. A locus is considered no-call if it is concordant for both
alleles but has a no-call on either allele. The "Allele concordance"
describes the comparison result on a per-allele basis.
OPTIONS
-h [ --help ]
Print this help message.
--reference arg
The input crr file.
--variants arg
The input variant file.
--genotypes arg
The input genotypes file.
--output-prefix arg
The path prefix for all output reports.
--reports arg (=Output,Verbose,Stats)
Comma-separated list of reports to generate. A report is one of:
Output The output genotypes file.
Verbose The verbose output file.
Stats The stats output file.
SUPPORTED FORMAT_VERSION
0.3 or later
-------------------------------------------------------------------------------
COMMAND NAME
calldiff - Compares two Complete Genomics variant files.
DESCRIPTION
Compares two Complete Genomics variant files. Divides the genome up into
superloci of nearby variants, then compares the superloci. Also refines the
comparison to determine per-call or per-locus comparison results.
Comparison results are usually described by a semi-colon separated string,
one per allele. Each allele's comparison result is one of the following
classifications:
ref-identical The alleles of the two variant files are identical, and
they are consistent with the reference.
alt-identical The alleles of the two variant files are identical, and
they are inconsistent with the reference.
ref-consistent The alleles of the two variant files are consistent,
and they are consistent with the reference.
alt-consistent The alleles of the two variant files are consistent,
and they are inconsistent with the reference.
onlyA The alleles of the two variant files are inconsistent,
and only file A is inconsistent with the reference.
onlyB The alleles of the two variant files are inconsistent,
and only file B is inconsistent with the reference.
mismatch The alleles of the two variant files are inconsistent,
and they are both inconsistent with the reference.
phase-mismatch The two variant files would be consistent if the
hapLink field had been empty, but they are
inconsistent.
ploidy-mismatch The superlocus did not have uniform ploidy.
In some contexts, this classification is rolled up into a simplified
classification, which is one of "identical", "consistent", "onlyA",
"onlyB", or "mismatch".
A good place to start looking at the results is the superlocus-output file.
It has columns defined as follows:
SuperlocusId An identifier given to the superlocus.
Chromosome The name of the chromosome.
Begin The 0-based offset of the start of the superlocus.
End The 0-based offset of the base one past the end of the
superlocus.
Classification The match classification of the superlocus.
Reference The reference sequence.
AllelesA A semicolon-separated list of the alleles (one per
haplotype) for variant file A, for the phasing with the
best comparison result.
AllelesB A semicolon-separated list of the alleles (one per
haplotype) for variant file B, for the phasing with the
best comparison result.
The locus-output file contains, for each locus in file A and file B that is
not consistent with the reference, an annotated set of calls for the locus.
The calls are annotated with the following columns:
SuperlocusId The id of the superlocus containing the locus.
File The variant file (A or B).
LocusClassification The locus classification is determined by the
varType column of the call that is inconsistent
with the reference, concatenated with a
modifier that describes whether the locus is
heterozygous, homozygous, or contains no-calls.
If there is no one variant in the locus (i.e.,
it is heterozygous alt-alt), the locus
classification begins with "other".
LocusDiffClassification The match classification for the locus. This is
defined to be the best of the comparison of the
locus to the same region in the other file, or
the comparison of the superlocus.
The somatic output file contains a list of putative somatic variations of
genome A. The output includes only those loci that can be classified as
snp, del, ins or sub in file A, and are called reference in the file B.
Every locus is annotated with the following columns:
VarCvgA The totalReadCount from file A for this locus
(computed on the fly if file A is not a
masterVar file).
VarScoreA The varScoreVAF from file A, or varScoreEAF if
the "--diploid" option is used.
RefCvgB The maximum of the uniqueSequenceCoverage
values for the locus in genome B.
RefScoreB Minimum of the reference scores of the locus in
genome B.
SomaticCategory The category used for determining the
calibrated scores and the SomaticRank.
VarScoreACalib The calibrated variant score of file A, under
the model selected by using or not using the
"--diploid" option, and corrected for the count
of heterozygous variants observed in this
genome. See user guide for more information.
VarScoreBCalib The calibrated reference score of file B, under
the model selected by using or not using the
"--diploid" option, and corrected for the count
of heterozygous variants observed in this
genome. See user guide for more information.
SomaticRank The estimated rank of this somatic mutation,
amongst all true somatic mutations within this
SomaticCategory. The value is a number between
0 and 1; a value of 0.012 means, for example,
that an estimated 1.2% of the true somatic
mutations in this somaticCategory have a
somaticScore less than the somaticScore for
this mutation. See user guide for more
information.
SomaticScore An integer that provides a total order on
quality for all somatic mutations. It is equal
to -10*log10( P(false)/P(true) ), under the
assumption that this genome has a rate of
somatic mutation equal to 1/Mb for
SomaticCategory snp, 1/10Mb for SomaticCategory
ins, 1/10Mb for SomaticCategory del, and 1/20Mb
for SomaticCategory sub. The computation is
based on the assumptions described in the user
guide, and is affected by choice of variant
model selected by using or not using the
"--diploid" option.
OPTIONS
-h [ --help ]
Print this help message.
--reference arg
The input crr file.
--variantsA arg
The "A" input variant file.
--variantsB arg
The "B" input variant file.
--output-prefix arg
The path prefix for all output reports.
--reports arg (=SuperlocusOutput,SuperlocusStats,LocusOutput,LocusStats)
Comma-separated list of reports to generate. (Beware any reports whose
name begins with "Debug".) A report is one of:
SuperlocusOutput Report for superlocus classification.
SuperlocusStats Report for superlocus classification stats.
LocusOutput Report for locus classification.
LocusStats Report for locus stats.
VariantOutput Both variant files annotated by comparison
results.If the somatic output report is
requested, file A is also annotated with the
same score ranks as produced in that report.
SomaticOutput Report for the list of simple variations that
are present only in file "A", annotated with
the score that indicates the probability of
the variation being truly somatic. Requires
beta, genome-rootA, and genome-rootB options
to be provided as well. Note: generating this
report slows calldiff by 10x-20x.
DebugCallOutput Report for call classification.
DebugSuperlocusOutput Report for debug superlocus information.
DebugSomaticOutput Report for distribution estimates used for
somatic rescoring. Only produced if
SomaticOutput is also turned on.
--diploid
Uses varScoreEAF instead of varScoreVAF in somatic score computations.
Also, uses diploid variant model instead of variable allele mixture
model.
--locus-stats-column-count arg (=15)
The number of columns for locus compare classification in the locus
stats file.
--max-hypothesis-count arg (=32)
The maximum number of possible phasings to consider for a superlocus.
--no-reference-cover-validation
Turns off validation that all bases of a chromosome are covered by
calls of the variant file.
--genome-rootA arg
The "A" genome directory, for example /data/GS00118-DNA_A01; this
directory is expected to contain ASM/REF and ASM/EVIDENCE
subdirectories.
--genome-rootB arg
The "B" genome directory.
--calibration-root arg
The directory containing calibration data. For example, there should
exist a file calibration-root/0.0.0/metrics.tsv.
--beta
This flag enables the SomaticOutput report, which is beta
functionality.
SUPPORTED FORMAT_VERSION
0.3 or later
-------------------------------------------------------------------------------
COMMAND NAME
listvariants - Lists the variants present in a variant file.
DESCRIPTION
Lists all called variants present in the specified variant files, in a
format suitable for processing by the testvariants command. The output is a
tab-delimited file consisting of the following columns:
variantId Sequential id assigned to each variant.
chromosome The chromosome of the variant.
begin 0-based reference offset of the beginning of the variant.
end 0-based reference offset of the end of the variant.
varType The varType as extracted from the variant file.
reference The reference sequence.
alleleSeq The variant allele sequence as extracted from the variant
file.
xRef The xRef as extrated from the variant file.
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
--reference arg
The reference crr file.
--output arg (=STDOUT)
The output file (may be omitted for stdout).
--variants arg
The input variant files (may be passed in as argument at the end of the
command).
--variant-listing arg
The output of another listvariants run, to be merged in to produce the
output of this run.
--list-long-variants
In addition to listing short variants, list longer variants as well
(10's of bases) by concatenating nearby calls.
SUPPORTED FORMAT_VERSION
0.3 or later
-------------------------------------------------------------------------------
COMMAND NAME
testvariants - Tests variant files for presence of variants.
DESCRIPTION
Tests variant files for presence of variants. The output is a tab-delimited
file consisting of the columns of the input variants file, plus a column
for each assembly results file that contains a character code for each
allele. The character codes have meaning as follows:
0 This allele of this genome is consistent with the reference at this
locus but inconsistent with the variant.
1 This allele of this genome has the input variant at this locus.
N This allele of this genome has no-calls but is consistent with the
input variant.
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
--reference arg
The reference crr file.
--input arg (=STDIN)
The input variants to test for.
--output arg (=STDOUT)
The output file (may be omitted for stdout).
--variants arg
The input variant files (may be passed in as arguments at the end of
the command).
SUPPORTED FORMAT_VERSION
0.3 or later
-------------------------------------------------------------------------------
COMMAND NAME
evidence2sam - Converts CGI variant evidence data into SAM format.
DESCRIPTION
The evidence2sam converter takes as input evidence mapping files
(evidenceDnbs-*) and generates one SAM file as an output. The output is
sent into stdout by default. By default, all the evidence mapping records
from the input are converted into a pair of corresponding SAM records - one
record for each HalfDNB. The negative gaps in CGI mappings are represented
using GS/GQ/GC tags.
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
-e [ --evidence-dnbs ] arg
Input evidence dnbs file.
-s [ --reference ] arg
Reference file.
-o [ --output ] arg (=STDOUT)
The output SAM file (may be omitted for stdout).
-r [ --extract-genomic-region ] arg
defines a region as a half-open interval 'chr,from,to'.
--keep-duplicates
Keep local duplicates of DNB mappings.All the output SAM records will
be marked as not primary if this option is used.
--add-allele-id
Generate interval id and allele id tags.
--skip-not-mapped
Skip not mapped records
--add-mate-sequence
Generate mate sequence and score tags.
--mate-sv-candidates
Inconsistent mappings are normally converted as single arm mappings
with no mate information provided. If the option is used map2sam will
mate unique single arm mappings in SAM including those on different
stands and chromosomes. To distinguish these "artificially" mated
records a tag "XS:i:1" is used. The MAPQ provided for these records is
a single arm mapping weight.
--add-unmapped-mate-info
works like add-mate-sequence, but is applied to inconsistent mappings
only
--primary-mappings-only
report only the best mappings
--consistent-mapping-range arg (=1300)
limit the maximum distance between consistent mates
SUPPORTED FORMAT_VERSION
0.3 or later
-------------------------------------------------------------------------------
COMMAND NAME
join - Joins two tab-delimited files based on equal fields or overlapping regions.
DESCRIPTION
Joins two tab-delimited files based on equal fields or overlapping regions.
By default, an output record is produced for each match found between file
A and file B, but output format can be controlled by the --output-mode
parameter.
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
--input arg
File name to use as input (may be passed in as arguments at the end of
the command), or omitted for stdin). There must be exactly two input
files to join. If only one file is specified by name, file A is taken
to be stdin and file B is the named file. File B is read fully into
memory, and file A is streamed. File A's columns appear first in the
output.
--output arg (=STDOUT)
The output file name (may be omitted for stdout).
--match arg
A match specification, which is a column from A and a column from B
separated by a colon.
--overlap arg
Overlap specification. An overlap specification consists of a range
definition for files A and B, separated by a colon. A range definition
may be two columns, in which case they are interpreted as the beginning
and end of the range. Or it may be one column, in which case the range
is defined as the 1-base range starting at the given value. The records
from the two files must overlap in order to be considered for output.
Two ranges are considered to overlap if the overlap is at least one
base long, or if one of the ranges is length 0 and the ranges overlap
or abut. For example, "begin,end:offset" will match wherever end-begin
> 0, begin<offset+1, and end>offset, or wherever end-begin = 0,
begin<=offset+1, and end>=offset.
-m [ --output-mode ] arg (=full)
Output mode, one of the following:
full Print an output record for each match found between
file A and file B.
compact Print at most one record for each record of file A,
joining the file B values by a semicolon and
suppressing repeated B values and empty B values.
compact-pct Same as compact, but for each distinct B value,
annotate with the percentage of the A record that is
overlapped by B records with that B value. Percentage
is rounded up to nearest integer.
--overlap-mode arg (=strict)
Overlap mode, one of the following:
strict Range A and B overlap if A.begin < B.end and
B.begin < A.end.
allow-abutting-points Range A and B overlap they meet the strict
requirements, or if A.begin <= B.end and
B.begin <= A.end and either A or B has zero
length.
--select arg (=A.*,B.*)
Set of fields to select for output.
-a [ --always-dump ]
Dump every record of A, even if there are no matches with file B.
--overlap-fraction-A arg (=0)
Minimum fraction of A region overlap for filtering output.
--boundary-uncertainty-A arg (=0)
Boundary uncertainty for overlap filtering. Specifically, records
failing the following predicate are filtered away: overlap >=
overlap-fraction-A * ( A-range-length - boundary-uncertainty-A )
--overlap-fraction-B arg (=0)
Minimum fraction of B region overlap for filtering output.
--boundary-uncertainty-B arg (=0)
Boundary uncertainty for overlap filtering. Specifically, records
failing the following predicate are filtered away: overlap >=
overlap-fraction-B * ( B-range-length - boundary-uncertainty-B )
SUPPORTED FORMAT_VERSION
Any
-------------------------------------------------------------------------------
COMMAND NAME
junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
DESCRIPTION
junctiondiff takes two junction files A and B as input and produces the
following output:
- "diff-inputFileName" - the junctions from an input file A that are not
present in input file B.
- "report.txt" - a brief summary report (if --statout is used)
Two junctions are considered equivalent if:
- they come from different files
- left and right positions of one junction are not more than "--distance"
bases apart from the corresponding positions of another junction
- the junction scores are equal or above the scoreThreshold
- they are on the same strands
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
-s [ --reference ] arg
Reference file.
-a [ --junctionsA ] arg
input junction file A.
-b [ --junctionsB ] arg
input junction file B.
-A [ --scoreThresholdA ] arg (=10)
score threshold value for the input file A.
-B [ --scoreThresholdB ] arg (=0)
score threshold value for the input file B.
-d [ --distance ] arg (=200)
Max distance between coordinates of potentially compatible junctions.
-l [ --minlength ] arg (=500)
Minimum deletion junction length to be included into the difference
file.
-o [ --output-prefix ] arg
The path prefix for all the output reports.
-S [ --statout ]
(Debug) Report various input file statistics. Experimental feature.
SUPPORTED FORMAT_VERSION
1.5 or later
-------------------------------------------------------------------------------
COMMAND NAME
junctions2events - Groups and annotates junction calls by event type.
DESCRIPTION
This tool searches for groups of related junctions and for every group
attempts to determine the event that caused the junctions. For example,
isolated strand-consistent intrachromosomal junction is likely to be caused
by a deletion event.
Every junction in the file specified by "junctions" parameter will be
annotated. Optionally, the tool can search for the related junctions in a
larger list of junctions specified by "all-junctions" parameter. For
example, one may use the high confidence junction file to restrict the list
of events to ones that contain at least one high-confidence junction, while
using the complete list of all junctions to make sure that even
low-confidence junctions will be taken into account when grouping the
junctions and determining the event type.
The output consists of two files, [prefix]AnnotatedJunctions.tsv and
[prefix]Events.tsv. The annotated junction file contains the junctions from
the primary input file annotated by the following columns:
EventId Integer id that links the junction file to the event
file
Type Type of the event that caused the junction
RelatedJunctions Semicolon-separated list of other junctions that were
grouped with this junction
The event list file contains the following columns:
EventId Unique id of the event
Type Type of the event. One of the following values:
artifact caused by a flaw in the reference
complex event involves multiple junctions and doesn't fit the
pattern of any simple event type
deletion deletion of the sequence described by the Origin columns
tandem-duplication tandem duplication of the origin sequence
probable-inversion inversion of the origin sequence that is
confirmed from one side of the inversion only
inversion inversion of the origin sequence replacing the sequence
described by the Destination columns, confirmed from both
sides
distal-duplication copy of the origin sequence into the area
described by the Destination columns
distal-duplication-by-mobile-element copy of the origin sequence
caused by a known active
mobile element
interchromosomal isolated junction between different chromosomes;
Origin and Destination columns describe the
reference loci that are brought together by this
event.
RelatedJunctionIds Semicolon-separated list of the junctions related to
this event.
MatePairCounts Semicolon-separated list that contains the read count
for every related junction.
FrequenciesInBaselineGenomeSet Semicolon-separated list that contains
the frequency in the baseline set of
genomes for every related junction.
OriginRegion[...] Description of the origin sequence of the event; the
exact semantics of "origin" depend on the event type.
DestinationRegion[...] Description of the destination region for the
event.
DisruptedGenes List of all genes that contain one or more of the
locations of the junctions grouped to this event.
ContainedGenes For the events that duplicate or remove regions of
sequence, this column contains the list of genes fully
contained within the deleted or copied region.
GeneFusions List of possible gene fusions described as GeneA/GeneB, and
fusions of regulatory sequence of one gene to another gene,
described as TSS-UPSTREAM[GeneA]/GeneB.
RelatedMobileElement For the duplication events caused by a mobile
element, this column contain the description of
the element in Family:Name:DivergencePercent
format, for example "L1:L1HS:0.5".
MobileElement[...] Location of the mobile element
All sequence intervals are described using zero-based, half-open
coordinates.
Repeat and gene data files necessary to run this command can be downloaded
from the Complete Genomics site:
ftp://ftp.completegenomics.com/AnnotationFiles/
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
--reference arg
Reference file.
--output-prefix arg
The path prefix for all output reports.
--junctions arg
Primary input junction file.
--all-junctions arg
Superset of the input junction file to use when searching for the
related junctions. The default is to use only the junctions in the
primary junction file.
--repmask-data arg
The file that contains repeat masker data.
--gene-data arg
The file that contains gene location data.
--regulatory-region-length arg (=7500)
Length of the region upstream of the gene that may contain regulatory
sequence for the gene. Junctions that connect this region to another
gene will be annotated as a special kind of gene fusion.
--contained-genes-max-range arg (=-1)
Maximum length of a copy or deletion event to annotate with all genes
that overlap the copied or deleted segment. Negative value causes all
events to be annotated regardless of the length.
--max-related-junction-distance arg (=700)
Junctions occurring within this distance are presumed to be related.
--max-pairing-distance arg (=10000000)
When searching for paired junctions caused by the same event, maximum
allowed distance between junction sides.
--max-copy-target-length arg (=1000)
Pairs of junctions will be classified as a copy event only if the
length of the implied copy target region is below this threshold.
--max-simple-event-distance arg (=10000000)
When given a choice of explaining an event as a mobile element copy or
as a simple deletion/duplication, prefer the latter explanation if the
length of the affected sequence if below this threshold.
--mobile-element-names arg (=L1HS,SVA)
Comma-separated list of the names of the mobile elements that are known
to be active and sometimes copy flanking 3' sequence.
--max-distance-to-m-e arg (=2000)
When searching for a mobile element related to a junction, maximum
allowed distance from the junction side to the element.
--max-related-junction-output arg (=100)
Maximum number of related junctions included into annotation field
SUPPORTED FORMAT_VERSION
1.5 or later
-------------------------------------------------------------------------------
COMMAND NAME
generatemastervar - Converts a variation file to a one-line-per-locus format.
DESCRIPTION
The output file contains one line for each locus in the input variation
file. The following columns are always present:
locus Locus ID, as in the input file.
chromosome The name of the chromosome.
begin The first base of the locus interval, 0-based.
end The first base past the locus interval, 0-based.
zygosity One of the following values:
no-call both alleles contain no-calls
half one allele fully called
hap haploid region
hom homozygous region
het-ref heterozygous region, one allele is reference
het-alt heterozygous region, neither allele is reference
varType For simple loci, one of "ref", "snp", "del", "ins" or
"sub". For more complex regions, "complex".
reference Reference sequence, or "=" for pure reference or pure
no call regions.
allele1Seq Sequence of the first allele, may contain "?" or "N"
characters for unknown-length and known-length
no-calls, respectively.
allele2Seq Sequence of the second allele.
allele1VarScoreVAF The varScoreVAF of the first allele. For pre-2.0
var files, which have totalScore instead of
varScoreVAF, this column is filled in with
totalScore. For the loci that contain multiple
calls, this is the minimum score across all calls.
allele2VarScoreVAF The varScoreVAF of the first allele. For pre-2.0
var files, which have totalScore instead of
varScoreVAF, this column is filled in with
totalScore. For the loci that contain multiple
calls, this is the minimum score across all calls.
allele1VarScoreEAF The varScoreEAF of the first allele. For pre-2.0
var files, which have totalScore instead of
varScoreEAF, this column is filled in with
totalScore. For the loci that contain multiple
calls, this is the minimum score across all calls.
allele2VarScoreEAF The varScoreEAF of the first allele. For pre-2.0
var files, which have totalScore instead of
varScoreEAF, this column is filled in with
totalScore. For the loci that contain multiple
calls, this is the minimum score across all calls.
allele1VarFilter The varFilter of the first allele. For pre-2.0 var
files, which do not have a varQuality column, this
field is empty. For multiple calls, this is the
union of varFilters across all calls.
allele2VarFilter The varFilter of the second allele. For pre-2.0 var
files, which do not have a varQuality column, this
field is empty. For multiple calls, this is the
union of varFilters across all calls.
allele1HapLink Haplink ID of the first allele. Alleles with the same
ID are known to reside on the same haplotype.
allele2HapLink Haplink ID of the second allele.
The allele to be placed first is chosen according to the following priority
list:
fully called variant allele;
fully called reference allele;
partially called allele;
completely no-called allele.
In addition to the mandatory columns above, various annotation columns can
be added to the file using "annotations" parameter. The supported
annotation sources and the corresponding additional columns are listed
below.
copy Adds column "xRef" that contains a concatenation of
all dbSNP annotations for this locus from the input
variant file. If the source file is already in
one-line-per-locus format, also copies over all other
annotations already present in the source.
evidence Adds columns:
evidenceIntervalId ID of the corresponding evidence interval.
allele1ReadCount Number of evidence reads that support the
first allele
allele2ReadCount Number of evidence reads that support the
second allele
referenceAlleleReadCount Number of evidence reads that support the
reference
totalReadCount Total number of evidence reads that overlap
the locus. This includes reads that don't show
strong support for either of the called
alleles.
ref Adds column "minReferenceScore" that contains the
minimum value of the reference score over the locus
interval extended by one base in either direction. Off
by default.
gene Adds columns "allele1Gene" and "allele2Gene" that
contain summarized information about the overlap and
impact on known genes. Derived from the gene
annotation in the CGI data package.
ncrna Adds column "miRBaseId" that contains summarized
information about overlap with non-coding RNA. Derived
from the ncRNA file in the CGI data package.
repeat Adds column "repeatMasker" that contains information
about the repeats overlapping the locus. Requires a
data file available from the Complete Genomics site:
ftp://ftp.completegenomics.com/AnnotationFiles/
segdup Adds column "segDupOverlap" that contains the number
segmental duplications overlapping the locus. Requires
a data file available from Complete Genomics site:
ftp://ftp.completegenomics.com/AnnotationFiles/
cnv Adds the cnvDiploid, cnvNondiploid and (if present)
cnvSomNondiploid annotations (described below), as
available in the CGI data package.
cnvDiploid Adds columns "relativeCoverageDiploid" and
"calledPloidy" derived from the diploid CNV call
details in the CGI data package.
cnvNondiploid Adds columns "relativeCoverageNondiploid",
"calledLevel", and, if present, "bestLAFsingle",
"lowLAFsingle", and "highLAFsingle" columns derived
from the nondiploid CNV call details in the CGI data
package.
cnvSomNondiploid Adds columns "relativeCoverageSomaticNondiploid", and
"somaticCalledLevel" columns derived from the somatic
nondiploid CNV call details in the CGI data package.
Additionally, "bestLAFpaired", "lowLAFpaired", and
"highLAFpaired" columns will be added, based on
columns with the same name, or, in the case of older
data packages, "bestLAF", "lowLAF", and "highLAF".
fisherSomatic Adds column "fisherSomaticScore" that contains an
alternative score indicating confidence in a somatic
variant call. The score is computed using one-tailed
Fisher's Exact Test on counts of reads supporting alt
and reference alleles in the baseline and non-baseline
samples. The given score is intended to have a
PHRED-like interpretation of -10*log10(probability of
an erroneous call), though details of the count
tabulation make the intended calibration only
approximate.
The column groups are added in the order they are listed in the
"annotations" command line parameter. By default the tool will attempt to
add all annotations. For older data packages that do not contain some of
the necessary files remove the corresponding annotation source from the
list.
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
--reference arg
The reference crr file.
--output arg (=STDOUT)
The output file (may be omitted for stdout).
--variants arg
The input variant file.
--annotations arg (=copy,evidence,gene,ncrna,repeat,segdup,cnv)
Comma-separated list of annotations to add to each line.
--genome-root arg
The genome directory, for example /data/GS00118-DNA_A01; this directory
is expected to contain an intact ASM subdirectory.
--repmask-data arg
The file that contains repeat masker data.
--segdup-data arg
The file that contains segdup data.
SUPPORTED FORMAT_VERSION
0.3 or later
-------------------------------------------------------------------------------
COMMAND NAME
varfilter - Copies input var file or masterVar file to output, applying specified filters.
DESCRIPTION
Copies input var file or masterVar file to output, applying specified
filters (which are available to all cgatools commands that read a var file
or masterVar file as input). Filters are specified by appending the filter
specification to the var file name on the command line. For example:
/path/to/var.tsv.bz2#varQuality!=VQHIGH
The preceding example filters out any calls marked as VQLOW. The filter
specification follows the "#" sign, and consists of a list of filters to
apply, separated by a comma. Each filter is a colon-separated list of call
selectors. Any scored call that passes all the colon-separated call
selectors for one or more of the comma-separated filters is turned into a
no-call. The following call selectors are available:
hom Selects only calls in homozygous loci.
het Selects any scored call not selected by the hom
selector.
varType=XX Selects calls whose varType is XX.
varScoreVAF<XX Selects calls whose varScoreVAF<XX.
varScoreEAF<XX Selects calls whose varScoreEAF<XX.
varQuality!=XX (Pre-2.4.0 var files) Selects calls whose varQuality is
not XX.
varFilter!=XX Selects calls whose varFilter is not XX.
varFilter contains XX|YY Selects calls whose varFilter contains XX or
YY.
Here is an example that filters homozygous SNPs with varScoreVAF < 25 and
heterozygous insertions with varScoreEAF < 50:
'/path/to/var.tsv.bz2#hom:varType=snp:varScoreVAF<25,het:varType=ins:varScoreEAF<50'
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
--reference arg
The reference crr file.
--input arg
The input var file or masterVar file (typically with filters
specified).
--output arg (=STDOUT)
The output file (may be omitted for stdout).
SUPPORTED FORMAT_VERSION
0.3 or later
-------------------------------------------------------------------------------
COMMAND NAME
mkvcf - Converts var file(s) or masterVar file(s) to VCF.
DESCRIPTION
Converts var file(s) or masterVar file(s) to VCF.
OPTIONS
-h [ --help ]
Print this help message.
--beta
This is a beta command. To run this command, you must pass the --beta
flag.
--reference arg
The reference crr file.
--output arg (=STDOUT)
The output file (may be omitted for stdout).
--field-names arg (=GT,PS,NS,AN,AC,AF,SS,FT,CGA_XR,CGA_ALTCALLS,CGA_FI,GQ,HQ,EHQ,CGA_CEHQ,GL,CGA_CEGL,DP,AD,CGA_RDP,CGA_ODP,CGA_OAD,CGA_ORDP,CGA_PFAM,CGA_MIRB,CGA_RPT,CGA_SDO,CGA_SOMC,CGA_SOMR,CGA_SOMS,CGA_SOMF,GT,CGA_GP,CGA_NP,CGA_CP,CGA_PS,CGA_CT,CGA_TS,CGA_CL,CGA_LS,CGA_LAFS,CGA_LLAFS,CGA_ULAFS,CGA_SCL,CGA_SLS,CGA_LAFP,CGA_LLAFP,CGA_ULAFP,GT,FT,CGA_IS,CGA_IDC,CGA_IDCL,CGA_IDCR,CGA_RDC,CGA_NBET,CGA_ETS,CGA_KES,GT,FT,CGA_BF,CGA_MEDEL,MATEID,SVTYPE,CGA_BNDG,CGA_BNDGO,CGA_BNDMPC,CGA_BNDPOS,CGA_BNDDEF,CGA_BNDP)
Comma-separated list of field names. By default, all fields are
included, but you may override this option to ensure only a subset of
the fields is included in the VCF output. For a description of each
field, see the cgatools user guide.
--source-names arg (=masterVar,CNV,SV,MEI)
Comma-separated list of source names. The following source names are
available:
masterVar - Includes records extracted from the masterVar file.
CNV - Includes CNV-related records.
SV - Includes records derived from junctions files.
MEI - Includes records describing mobile element insertions.
Some of these source types are only available for more recent pipeline
versions, and some of these source types do not support multi-genome
VCFs. For more information about which source types are available for
which versions of the Complete Genomics pipeline software, see the
cgatools user guide.
--genome-root arg
For each genome to include in the VCF, the genome root directory, for
example /data/GS00118-DNA_A01; this directory is expected to contain
the ASM and LIB subdirectories, for example. You must supply this
option for each genome in the VCF, unless you are using
--source-names=masterVar and you have specified the --master-var option
for each genome in the VCF.
--master-var arg
For each genome to include in the VCF, the masterVar file. If
genome-roots parameter is given, this parameter defaults to the
masterVar in the given genome-root.
--include-no-calls
Small variants VCF records include loci that have no
reference-inconsistent calls.
--calibration-root arg
The directory containing calibration data. For example, there should
exist a file calibration-root/0.0.0/metrics.tsv. This option is only
required if CGA_CEHQ or CGA_CEGL are included in the --field-names
parameter.
--junction-file arg
For each genome to include in the VCF, the junctions file. If
genome-roots parameter is given, this parameter defaults to the
respective junctions file in the export directory.
--junction-score-threshold arg (=10)
Junction score thresholds (discordant mate pair count).
--junction-side-length-threshold arg (=70)
Junction side length threshold.
--junction-distance-tolerance arg (=200)
Distance tolerance for junction compatibility.
--junction-length-threshold arg (=500)
Length threshold for compatible junctions.
--junction-normal-priority
Normal junction priority for vcf output.
--junction-tumor-hc
use high confidence junctions for tumors.
SUPPORTED FORMAT_VERSION
0.3 or later