Configuration controls can be placed inside a box on the configuration page. This setting is decorative only, but can make a busy page look more cohesive. Not all track types currently support this feature, but the most common types do, including wig, bigWig, bed, and bigBed. DEFAULT: off.
Example:
boxedCfg on
canPack <off/on>NOT FOR HUBS. Deprecated.
+Deprecated. The track type usually implies whether pack and + squish are offered, so this setting is rarely needed.
Most tracks can be displayed in all five
visibilities modes. However on some track types such as
wiggles, the squish and pack modes offer no real advantage
over the dense and full modes. By default, these tracks will
not offer the squish and pack vilibility settings.
Nevertheless, you can make your track offer
these visibility choices by turning canPack on. Note: subtracks
of composites will always offer all five choices.
Example:
canPack on
color <red,green,blue>Many track types allow the color of the data displayed in the image to be specified with @@ -540,31 +573,30 @@
chromosomes <chr1,chr2,...>Some datasets do not contain data for all chromosomes of a genome. When this is true, use this setting as a comma-separated list of the chromosomes that are covered. The system displays a message that no data is available when the user browses chromosomes not included in this list.
Example:
chromosomes chr1,chr7,chr18,chr19,chr22,chrX,chrM
configureByPopup <on/off>NOT FOR HUBS.
Most track displays that can be configured by a user can also be configured from directly within the Browser image through a right-click option that pops up a configuration dialog. While this functionality works on the majority of track types, some configuration dialogs are too complex or have too much embedded javascript control to be reliably configured through a pop-up. To turn off the ability to configure the track via right-click, change this setting to "off". The user will still be able to configure the track on the track's configuration page. DEFAULT: on.
Example:
configureByPopup off
Example:
otherDb mm10
This example sets the second assembly in the alignment to the mouse mm10 assembly.
otherTwoBitUrl <url/relativePath>For pairwise alignment tracks this can specify where to find the query sequence This setting can be used in psl, bigPsl, chain, and bigChain tracks.
Example:
otherTwoBitUrl https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
origAssembly <db>NOT FOR HUBS.
The original assembly version for which the dataset was generated. Datasets generated by mapping to one genome assembly may prove useful enough to map to a more recent assembly. Ideally datasets will be regenerated to map to the new assemblies coordinates, but sometimes this is not practical or expedient. Therefore, the dataset may have its genome coordinates "lifted over" to the more recent assembly. In some cases this results in an inferior but nevertheless useful representation. Such datasets should have their original assembly defined with this setting.
Example:
origAssembly hg18
type broadPeaktype coloredExontype gvftype ld2type narrowPeaktype peptideMappingEach of these is a specialized variation of the bed format. Their specialized definitions should be sought elsewhere. However, these item tracks share many of the same configuration options available to bed tracks.
An example can be found below.
-bigDataUrl2 <url/relativePath>This setting is for remote data file type - tracks (e.g. bigWig) and is fully described in the "Common - trackDb settings" portion of this document.
-colorByStrand <red,green,blue> <red,green,blue>To color items
differently by the strand they align to, use the colorByStrand
setting. The first color will be used for plus strand alignments
and the second for the minus strand. This setting is incompatible with spectrum
and all items on the same strand will have the same color, regardless of the item's
score.
Example:
colorByStrand 255,0,0 0,0,255
Plus strand alignments will be colored red, and minus
strand alignments will be blue. This setting is incompatible with spectrum,
and therefore all items on the same strand will have the same color, regardless of the item's
score.
Example:
labelOnFeature on-
exonArrows <on/off>On tracks that show exons or blocks within features, exon arrows allow the user to jump to the next exon or block outside the image. Exon arrows are typically shown by default in these types of tracks, with the exception of tracks in the Regulation group. The arrows can be explicitly shown or hidden using this setting.
Example:
exonArrows off
exonNumbers <on/off>A mouseover that shows the exon and intron numbers can be explicitly shown or hidden using this setting. The default is "on" for the track types genePred and bigGenePred.
Example:
exonNumbers off
The text can be set with the options "exonText" and "intronText". It defaults to "exon" and "intron", respectively.
<column>Filter <low>[:<high>]scoreFilter <low>[:<high>]pValueFilterqValueFiltersignalFilter<column>FilterLimits <low>[:<high>]<column>FilterByRange <off/on>
A number of
numerical filters are available for bed tracks. These are
conveniently named by the field that is filtered on. The most
common numerical filter is based on the standard bed field
score, and is thus controlled by the scoreFilter
setting. Other examples are pValueFilter, qValueFilter and
@@ -1549,35 +1572,33 @@
can be replaced with filter.score 400 and filterByRange.score 0:1000.
The advantage of switching to the filter.<fieldName> approach is that filters
can also be added on additional bigBed <fieldNames> such as filterText.disease
or filterValues.cellType where bigBeds defined with a disease or cellType column can
be filtered. See filter.<fieldName> for more information and examples.
Example:
scoreFilter 300
scoreFilterLimits 200:1000
The standard bed
field of score, which is an integer will be used to filter items
in the track. By default, items with scores below 300 will be
excluded. The filter cannot be set to less than 200 or more than 1000..
filterBy <field1:title=[+]opt1a...>
[field2:title=[+]opt2a...]NOT FOR HUBS. Not yet supported by bigBeds
Another method of
filtering items relies upon discrete values. One or more fields
such as name or score may contain a limited number
of discrete values that can be filtered on. These discrete values will be
displayed in a dropdown list from which the user can choose one or
more options. While the maximum number of options in the list is
not limited, displaying too many options can be confusing for the user.
Setting complexities:
_'
(underscore) character.=' (equal sign).type bigBed tracks, this setting can never
be larger than the hg.conf setting bigBedMaxItems, which by default is 100,000 at UCSC.
bigBedMaxItems is configured globally for a Genome Browser server and sets an upper limit on how many features can be loaded at most from a bigBed file, to avoid a single track making a Genome Browser view unusable at high zoom levels so it the upper limit for all maxItems settings of any tracks shown on a Genome Browser. If you have feedback on these values, please do not hesitate to contact us.
Example:
maxItems 25
maxWindowCoverage <integer>When too many individual bed items might be shown in the Browser image
(such as might occur when a large region of a chromosome is viewed),
maxWindowCoverage will switch the track into density coverage plot when
the window contains more than the specified number of bases.
Example:
maxWindowCoverage 10000000
Browser images that show more than 10,000,000 bases will result in the track data being displayed as a density coverage graph.
maxWindowToDraw <integer>When too many individual bed items might be shown in the Browser image
(such as might occur when a large region of a chromosome is viewed),
maxWindowToDraw will trigger a choice to display a message
asking users to zoom in to a smaller region.
Depending on the current visibility
of the bed track and which other tracks are being shown concurrently, the
Browser may automatically reduce the display to pack or dense mode in some cases.
The maxWindowToDraw setting allows you to force users to zoom in
as an overriding message will block out the data display. Unlike the maxItems
setting, which controls the display of vertical space and forces a display to dense
when the maximum number of items is exceeded, the maxWindowToDraw
setting dictates the number of bases to be displayed in a window
before the track is obscured with a message explaining the
requirement for zooming-in. Even without this setting,
there are browser operations that will ultimately prevent too many items from
being displayed by forcing a visualized summary in dense mode as noted.
Example:
maxWindowToDraw 10000000
Browser images that show more than 10,000,000 bases will result in the track data
being obscured with a note across the genomic range stating the message
zoom in to <= 10,000,000 bases to view items.
minGrayLevel <1-9>When a bed track contains the standard
field score, and when that score is used
to present items in gray or color scale (see
spectrum),
this setting specifies the lightest shade to be used.
This prevents the lowest scores from being displayed in too light of a color to easily
view. Set the value in the range 1 - 9, lightest to darkest.
Example:
minGrayLevel 4
This sets the lowest scores to slightly less than medium gray, while the highest scores appear black.
noScoreFilter onBy default, bed
tracks with 5 or more standard bed fields that contain either a '.' or
a '+' in the type setting will be filterable on score;
that is, they will have an assumed setting of "scoreFilter 0". To turn
this old-style default off, include the "noScoreFilter" setting.
Example:
type bigBed 6 +
noScoreFilter on
useScore 1Deprecated. Use spectrum instead.
+Shades each item by its score field, so low scores draw in light gray and
+ high scores draw near black. spectrum on does the same thing and is the
+ spelling to use in a new track. The Browser treats the two names as one setting, and
+ scoreMin, scoreMax and
+ minGrayLevel tune both the same way.
In a trackDb file or a hub, any value turns the shading on, including
+ useScore 0, because the Browser only checks whether the setting is present.
+ In a custom track the value is read, and 0 turns the shading off.
Example:
+useScore 1+
spectrum onscoreMax <integer>scoreMin <integer>Replaces useScore.
If your track is a
bed 5 or greater, then the standard bed score
field exists. This score, which is expected to vary from 0-1000,
can be used to control the shading of bed items drawn in the Browser
image. To activate this feature, set spectrum on.
Lower scores will be shaded in light gray by default, while higher
scores will trend towards black. This can be modified in a number of ways:
Specifies where item sequence can be found (if any) so that item sequence, or differences from genomic sequence, can be drawn when viewing a sufficiently small region.
extFile is
specified, two additional parameters are required, the name of
the seq table followed by the name of the extFile table to use
in looking up the sequence. These tables are loaded by hgLoadSeq.
nameIsSequence is specified then the 4th column (name or
sequence) contains the sequence. (see
hg/lib/encode/tagAlign.as)seq1Seq2
is specified then the 7th & 8th columns (seq1 and seq2)
contain the left and right pairs of the sequence. (see
hg/lib/encode/pairedTagAlign.as)ss is specified then a
user-provided blat sequence is looked for.2bit is specified then looks for sequence in the file specified
by the otherTwoBitUrl tag.
baseColorUseCds <given>Specifies where coding sequence (CDS) coordinates can be found (if any) so that codons can be drawn when viewing a sufficiently small region.
Example:
baseColorUseCds given
baseColorDefault
<diffBases/diffCodons/itemBases/itemCodons/genomicCodons>Specifies the default drawing mode.
The itemBases, itemCodons, diffBases and
diffCodons options are applicable only if the track has sequence, as
specified by the baseColorUseSequence setting.
The genomicCodons, itemCodons and diffCodons are
applicable only if the track has CDS info, as specified by the baseColorUseCds
setting.
baseColorTickColor <lighterShade/contrastingColor>NOT FOR HUBS. Not yet supported by bigBeds
-Choose a contrastingColor (this is often
- white) or lighterShade of color. This should be the
- same color as would be chosen for the base text if the user were
- zoomed in to base level.
Sets the color of the tick marks that mark where item bases differ from the
+ genome. Those marks appear when the track draws with
+ baseColorDefault diffBases and the view is zoomed out past base
+ level. Their default color is red.
contrastingColor: a color that stands out against the item
+ color, often white.lighterShade: a lighter version of the item color.Both values are worked out from the item's own color, so this setting does
+ nothing unless the track gives each item a color. In a hub the way to do that is
+ colorByStrand. Without it the
+ setting is read and ignored, and the tick marks stay red.
+ itemRgb does not count here: it colors an item as it is drawn, but
+ it does not give the track the per-item color this setting reads.
Example:
++ colorByStrand 0,0,200 200,0,0 + baseColorDefault diffBases + baseColorTickColor contrastingColor
showDiffBasesAllScales onShow base differences for all zoom levels.
showDiffBasesMaxZoom <basesPerPixel>Show annotations highlighting base or codon differences
only if current zoom level does not exceed
basesPerPixel (a float). showDiffBasesAllScales
should also be set to make this useful.
showCdsAllScales onShow CDS for PSL tracks at all zoom levels.
showCdsMaxZoom <basesPerPixel>Use this setting (a float) to specify the maximum zoom-out allowed for displaying the CDS
for psl tracks.
In conjunction with this setting, showCdsAllScales must be set on and
showDiffBasesMaxZoom
should be set to a value not more than showCdsMaxZoom to make this
display configuration useful.
baseColorDefault genomicCodons
baseColorUseCds given
showDiffBasesMaxZoom 10000.0
showCdsMaxZoom 10000.0
baseColorUseCds table hgFixed.transMapGeneUcscGenes
baseColorUseSequence lfExtra
baseColorDefault diffCodons
baseColorTickColor lighterShade
showDiffBasesAllScales .
showCdsAllScales .
exonArrowsDense <off/on>On tracks that show exons or blocks within items, exon arrows allow the user to jump to the next exon/block outside the image. Use this setting to display exon arrows even when the track is in dense mode.
itemDetailsHtmlTable <table>NOT FOR HUBS. Supplemental table must be in local database.
Use this setting to specify a table, indexed by item name, that contains an optional HTML fragment to display on the details page for this item. The expected columns in the table are "name" and "html".
Example:
itemDetailsHtmlTable pseudoGeneDetails
itemImagePath <path> <suffix>itemBigImagePath <path> <suffix>Items can be
associated with images and the images can be made visible with
these two settings. The itemImagepath specifies a
URL path to a directory with image files named in the format
{name}.{suffix}. The name is retrieved from the table or remote data
file. This image will be displayed on the item detaiIs page. If
itemBigImagePath is also supplied, then a link to a
larger image will be provided. If the path provided is local to
the browser then the path should be relative.
Example:
@@ -2677,31 +2728,31 @@
the image images/myTrackImages/fred.png and will also
provide a link to a larger image at
http://bigImages.com/myTrackImages/fred.jpg.
mafTrack <trackName>NOT FOR HUBS
By specifying a multiple alignments track, the item details page will illustrate the differences for that item across a number of species.
Example:
mafTrack multiz46way
nextExonText <str>prevExonText <str>For tracks that offer multiple block items such as gene models, the next/previous exon arrows are usually displayed by default in the Browser. The functionality of these tiny arrows is described by mouse-over "tool tips" that default to "Next Exon" and "Prev Exon". If the blocks do not represent exons, you can adjust the tool tip text to the appropriate information with these two settings.
Example:
nextExonText "Next Match"
prevExonText "Previous Match"
maxHeightPixels <max:default:min>The amount of vertical viewing space for your signal track should be declared, though it is configurable by the user. Typically it is set to no more than 100 pixels and no less than 8, with a default of 16 or 32 pixels.
Example:
maxHeightPixels 100:16:8
The browser will display the track as 16 pixels high, but the user can scale it up to 100 pixels.
maxWindowToQuery <integer>For bigWigs only
When signal data is clicked in the Browser image, the details of the signal in the current viewing window are displayed. For bigWigs that reference remote data, the query can be a very expensive operation if the current window is large. To avoid overburdening the Browser, the size of the window to query should be limited. The value of this setting is the maximum window size in bases that should be queried to give the detailed signal numbers.
negateValues <on>Negate the values in the wiggle, meaning that positive values become negative and vice-versa. This is useful for wiggles representing transcription or other activities on the Crick strand. Be aware that wiggles with negative values are drawn in altColor not color as @@ -3364,52 +3415,52 @@
autoTranslate 0By default, a
predicted protein translation is generated for a gene model when
a user views it on the details page. This feature may be blocked
by setting autoTranslate to zero.
Example:
autoTranslate 0
The genPred track will NOT show auto-generated protein sequence, perhaps because this track is for RNA genes.
intronGap <#bases>In drawing gene models, it can be useful to see "exon arrows" when the transcript extends beyond the current window. This setting, which defaults to zero, ensures that these arrows will not be drawn if the interceding intron gap is less than the stated number of bases.
Example:
intronGap 12
Don't draw exon arrows when the gap between exons is 12 bases or less.
defaultLinkedTables <table1>[,table2...]In hgTables, when selecting output fields, display these all.joiner-linked tables by default.
Example:
defaultLinkedTables kgXref
idXref <idColumn> <altIdColumn>By using this setting you can link alternative names to the gene models found in a genePred. This is used by the Table Browser to establish links to other tables.
Example:
track knownGenes
idXref kgAlias kgID alias
The ID in the name column of the knownGenes table is related to the alias found in the kgAlias table.
oldToNew <tableName>In successive versions of gene models, it can @@ -3748,44 +3799,30 @@
type psl xeno loxAfr1
otherDb loxAfr1
colorChromDefault off
pred <assembly.table>Use the pred setting to name an assembly and table containing protein sequence data for the named alignments.
Example:
pred hg18.blastKGPep04
pslSequence <no/all/different>This setting specifies some display configuration options for - psl tracks that also have sequence loaded. -
all: Display nucleotide labels on all bases.different: Label only base differences. no: Allow the user to select which of the other two options is preferred.Example:
-pslSequence different-
transMapGene <assembly.table>transMapInfo <table>transMapSrc <assembly.table>transMapTypeDesc <label>For alignment tracks generated using the TransMap cross-species alignment algorithm, these settings are used to connect the transMap detailed information with the alignments.
transMapInfo: Use to name the table in the current assembly that
ties an alignment with the source assembly and feature. transMapSrc: Use
to name the table in the source species assembly that contains
the details of the feature's source location.
@@ -3922,31 +3959,31 @@
Example can be found below.
type netAlign <otherDb> <otherChainTable>otherDb <otherDb>Tracks of type netAlign show the best chains of
sequence alignments from another species to the reference genome.
Gaps are filled in levels, where possible. This type requires the
assembly database of the other species to be named in both the type setting and
in the "otherDb" setting.
Example can be found below.
chainColor <scheme>By default chains are colored by the alignment chromosome of the query species. This can be overridden with this setting. The three options are:
Chromosome - defaultNormalized Score - chains are colored by scoreBlack - no coloring occursThis setting affects
chain but not netAlign type tracks.
Example:
chainColor Black
Example:
chainLinearGap medium
chainMinScore <#>The chainMinScore setting should reflect the
"-minScore" parameter used in axtChain to generate the
track. It represents the score threshold for chains to be
included in the set. Default is 1000. This setting is for both
chain and netAlign type tracks.
Example:
chainMinScore 5000
chainNormScoreAvailable <yes/no>A given chain or netAlign track may or may not
have a populated normScore column. If the column exists, then
its value can be displayed in the item details page of the
Browser by setting chainNormScoreAvailable to yes.
Item coloring based upon score as selected by the
chainColor Normalized Score setting also requires
this setting to be yes.
Example:
chainNormScoreAvailable yes
chainColor Normalized Score
frames <table/url>A wigMaf or bigMaf track can display gene codon translation. The reading frame may differ between species. By providing the reading frames information in a separate table, the user can choose which frame to use when viewing the data. For bigMaf the value is expected to be a bigBed, for wigMaf it should be a table. Read about bigMaf supporting files on the help page.
Example:
frames myCodonFrames
frames myCodonFrames.bb
irows offBy default, gaps in the non-reference species are filled with the placeholder character:
-': No bases in the aligned species. Possibly
due to a lineage-specific insertion between the aligned blocks in the human genome
or a lineage-specific deletion between the aligned blocks in the aligning species.=': Aligning species has one or more unalignable
bases in the gap region. Possibly due to excessive evolutionary distance between
species or independent indels in the region between the aligned blocks in both species.irows to "off".
Example:
irows off
itemFirstCharCase noChangeThis controls if
species names in the multiple alignment should be capitalized in
the pairwise display. Set "noChange" to avoid forcing
the first letter to lower case.
Example:
itemFirstCharCase noChange
pairwiseHeight <#>A wigMaf display in the Browser image is a stacked set of pairwise alignments to the target genome. Using this setting, you can change the height of each pairwise signal in the image.
Example:
pairwiseHeight 10
speciesCodonDefault <species>This setting, which is used with "frames", declares the default species for the codon reading frame.
Example:
speciesCodonDefault hg19
frames myCodonFrames
speciesDefaultOff <species1> [species2 ...]To control which of
the stacked pairwise alignments are displayed or hidden by default, use
speciesDefaultOff to list the species alignments that will not be
displayed. Each species is specified as in the MAF
file Organism names except embedded dots and/or spaces
are replaced with underscores (e.g. C. elegans ->
c_elegans).
Example:
speciesDefaultOff galGal2 fr1 danRer1
speciesOrder <species1> [species2 …]Use speciesOrder to declare the order of the
stacked alignments. If there are many species in your track,
it may make sense to use the speciesGroups setting instead.
speciesLabels <species1=newLabel1> [species2=newLabel2 …]Use speciesLabels to specify new labels that map to sequence names.
Example:
speciesLabels mm10=mouse_mm10 mm39=mouse_mm39
speciesGroups <sgroup1> [sgroup2 …]sGroup_<sgroupN> <species1> [species2 …]You can include a list of "clades"
to group the species into. This option is an alternative to
speciesOrder, used when there are many species. Each
speciesGroup in the list must have its own setting
(sGroup_<group>), followed by a list of species,
specified as for speciesOrder.
speciesOrder panTro1 canFam1 mm5 rn3 \
galGal2 fr1 danRer1
speciesGroups Mammal Vertebrate
sGroup_Mammal mm9 rn4
sGroup_Vertebrate galGal2 fr1 danRer1
Choose one of these two alternatives to display species.
speciesUseFile <fileName>speciesUseFile <cartVariableName>Deprecated
Much more rarely used, this setting can
replace speciesOrder and speciesGroups.
- Set the speciesUseFile to a path relative to the apache cgi-bin.
- The file should contain a single species name as the first word of each line.
Example:
-speciesUseFile speciesLists/conserved8Way.txt+
speciesUseFile myTrack.speciesList
summary <tableName/url>This setting contains a table name containing a MAF summary table, or a url that points to a
bigBed containing that information. The summary
view is used when the browser display is zoomed out to contain a million
or more basepairs. A summary table is created from a multiple alignment MAF
file using the utility hgLoadMafSummary (SQL track) or
mafToBigMafSummary (bigMaf). For bigMaf, the value is assumed to be bigBed,
Read about bigMaf supporting files on the help page.
Example:
summary hg17Maf8waySummary
treeImage <imageFile>The phylogenetic tree can used to show the relations of the species in the multiple alignment should be included as an image file. This path is relative to the htdocs images directory (usually /images).
Example:
treeImage phylo/hg17Maf8way.jpg
wiggle <table1> <leftLabel1> <uiLabel1>
[table2 leftLabel2 uiLabelN ...]Optionally more than one conservation signal can be included with your MAF display by using this setting. When you include conservation wiggles, you @@ -4828,86 +4868,86 @@ for a complete description of how to prepare and display VCF data.
type vcfTabixIf the bigDataUrl setting is included, the data at the location
specified by that URL will be
displayed. Otherwise, a database table with a single column fileName
can specify the location of a local file or a URL.
If the database table includes a column seqName, a different
VCF file or URL can be specified for each assembly sequence.
Example can be found below.
hapClusterEnabled <true|false>If the VCF file includes genotype columns for at least two individuals, then a haplotype sorting display is enabled by default. This option can be used to disable it if desired, for example if the genotypes have not been phased and a significant portion of the genotypes are heterozygous. More information about the haplotype sorting display can be found on our Configuring VCF tracks page.
hapClusterMethod <centerWeighted|fileOrder|treeFile url>Assuming hapClusterEnabled is true, this specifies how
genotypes are ordered for display:
centerWeighted: For diploid organisms, this separates the two haplotypes
from each sample and dynamically clusters all haplotypes by similarity, weighted by
proximity to a central variant. The clustering tree will be drawn in the left label area.
This works best for phased genotypes.
fileOrder: Genotypes are displayed in the order in which they appear in
the VCF file.
treeFile url: Genotypes are displayed in the order in which they
appear in url, a
Newick-formatted tree file
whose leaf node IDs are the same as the genotype column IDs in the VCF file.
The tree will be drawn in the left label area.
hapClusterColorBy <altOnly|function|refAlt|base>Assuming hapClusterEnabled is true,
this specifies one of three ways that reference and alternate alleles are colored:
altOnly: reference allele is white (invisible),
alternate allele is black. This emphasizes haplotypes with alternate alleles. (default)
function: If the geneTrack setting is also provided, then
reference allele is white (invisible) and alternate allele is red if the variant changes
the protein sequence of a gene, green if the variant falls within a gene but does not
change the protein sequence, blue if the variant falls within the UTR of a protein-coding
gene or within a non-coding gene, and black if intronic or intergenic.
refAlt: reference allele is blue, alternate allele is red.
base: A is red, C is blue, G is green and T is magenta.
geneTrack <track>This is for use with hapClusterColorBy function; it specifies the gene track
to use when determining the functional effect of each variant.
hapClusterTreeAngle <triangle|rectangle>Assuming hapClusterEnabled is true,
this controls the shape of leaf clusters on the right of the tree
(i.e. the lines drawn to denote groups of identical local haplotypes):
triangle for the < shape (default), rectangle
for the [ shape.
labelFields <fieldName[,fieldName]>A list of fields from the bigBed based file that can be used as a label. The special value none can be specified if no labels are desired.
labelSeparator <text>One or more characters to use as the field separator between multiple labels. A slash (/) by default, this string can have double quotes around it if it should have white spaces in it.
showSnpWidth <integer>The maximum width (in bases) of a window where the halSnake will show SNPs between the reference and the other species.
hapClusterHeight <N>Assuming hapClusterEnabled is true,
this specifies the height in pixels of the haplotype sorting display.
applyMinQual <true|false>If true, then variants whose QUAL column contains a value less
than the minQual setting will not be displayed.
minQual <Q>
Assuming applyMinQual is true,
this is the minimum QUAL value required for a variant to be displayed.
minFreq <F>The minimum minor allele frequency required for a variant to be displayed. By default this is 0.0 (i.e. display all variants).
vcfDoFilter <on/off>Turn on/off the FILTER options available by default for VCF tracks
tag: Used in the code to select
and sort subtracks based upon their membership. Tag names
must be alphanumeric, begin with a letter, not contain a period, and be formed
such that the desired sort order of the member subtracks will result.title: Label of the subgroup as it appears on the
selection matrix that is displayed to the user, e.g.,"Antibody". Spaces within
titles must be replaced by '_'. A limited amount
of HTML is allowed in titles, such as the insertion of Greek letters using an HTML
code. Any use of HTML should be tested to ensure that it displays correctly.Because subgroup settings are often lengthy, it is recommended that the
'\' line continuation character be used to break up the setting over
multiple lines for easier reading.
noInherit onDeprecated.
+Placed on a subtrack, this stops the subtrack from taking settings from its composite
+ parent. Without it a subtrack inherits the parent's type and
+ group, plus every parent setting the subtrack does not define itself.
The Browser only checks whether the setting is present, so any value turns it on,
+ including noInherit off. Defining a setting on the subtrack already
+ overrides the inherited value, so this setting is rarely needed.
Example:
+noInherit on+
subGroups <gTag1=mTag1?> [gTag2= mTag2?]The subtracks themselves declare their
membership in a group with the subGroups setting.
Each subtrack must declare its membership in all of its
composite's subgroups. Notice that membership is declared
by pairs of tags: the group tag (e.g. gTag1) is paired with that
group's member tag (e.g. mTag1b) as gTag1=mTag1b (cell=K562).
dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]In order to define the type of UI desired for selecting subtracks based upon groups, additional settings are needed at the composite level. For a one- or two-dimensional array of