6d02024d6f5b80437784b274ff2ccf6940dde976 mspeir Wed Sep 9 15:08:26 2026 -0700 VCF help: document geneTrack, the function coloring scheme, and vcfPhasedColorBy, refs #38010 The rest of the settings vcfUi.c reads from trackDb but neither help page mentioned. geneTrack (vcfUi.c:269 and :681) is the gate for the functional-effect coloring in both the haplotype display and the trio display: the radio button is only printed when the setting is non-empty. Nothing on either page said so, so the scheme was undiscoverable and its absence looked like a bug. hapClusterColorBy therefore has four values, not the three both pages listed -- hgVcfTrackHelp.html went as far as saying "There are three ways that reference and alternate alleles can be colored" above three bullets. Add the fourth, in the order vcfCfgHapClusterColor prints the buttons, and add function to the value lists in vcf.html. vcfPhasedColorBy (mendelDiff|deNovo|function|noColor) was documented nowhere at all, not even in trackDbLibrary.shtml, though vcf.html already described what it does in the alt text of the trio screenshot. Add it to the trio settings. Both settings tables needed a wider value column to fit, so those rows are repadded; no wording in them changed. Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html index cac60b53e20..d64733d79ff 100755 --- src/hg/htdocs/goldenPath/help/vcf.html +++ src/hg/htdocs/goldenPath/help/vcf.html @@ -141,54 +141,55 @@ bigDataIndex attribute in the track line to point to the index file.

track type=vcfTabix name="My VCF" bigDataUrl=http://myorg.edu/mylab/my.vcf.gz bigDataIndex=http://myorg.edu/someOtherDirectory/myvcf.gz.tbi

Paste the custom track line into the text box in the custom track management page, click "submit" and view in the Genome Browser.

Parameters for VCF custom track definition lines

All options are placed in a single line separated by spaces (lines are broken only for readability here):

track type=vcfTabix bigDataUrl=http://...
     hapClusterEnabled=true|false
-    hapClusterColorBy=altOnly|refAlt|base
+    hapClusterColorBy=altOnly|function|refAlt|base
     hapClusterTreeAngle=triangle|rectangle
     hapClusterHeight=N
     applyMinQual=true|false minQual=Q
     minFreq=F
     name=track_label
     description=center_label 
     visibility=display_mode
     priority=priority
     db=db maxWindowToDraw=N 
     chromosomes=chr1,chr2,...

Note if you copy/paste the above example, you must remove the line breaks. Click here for a text version that you can paste without editing.

The track type and bigDataUrl are REQUIRED:

type=vcfTabix bigDataUrl=http://myorg.edu/mylab/my.vcf.gz

The remaining settings are OPTIONAL. Some are specific to VCF:

hapClusterEnabled   true|false                   # if file has phased genotypes, sort by local similarity
-hapClusterColorBy   altOnly|refAlt|base     # coloring scheme, default altOnly, conditional on hapClusterEnabled
+hapClusterColorBy   altOnly|function|refAlt|base # coloring scheme, default altOnly, conditional on hapClusterEnabled
 hapClusterTreeAngle triangle|rectangle           # draw leaves as < or [, default <, conditional on hapClusterEnabled
 hapClusterHeight    N                            # height of track in pixels, default 128, conditional on hapClusterEnabled
+geneTrack           track name                   # gene track used by the function coloring scheme; without it that scheme is not offered
 applyMinQual        true|false                   # if true, don't display items with QUAL < minQual; default false
 minQual             Q                            # minimum value of Q column to display item, conditional on applyMinQual
 minFreq             F                            # minimum minor allele frequency to display item; default 0.0

These VCF settings are also recognized. They are used mainly in track hubs and are rarely needed in a custom track line:

hapClusterMethod centerWeighted|fileOrder|treeFile url # haplotype sort order, default centerWeighted
 sampleColorFile  url                                   # sample-to-color table, used with hapClusterMethod treeFile
 minAc            N                                     # minimum alternate allele count to display item; default 0
 vcfDoQual        true|false                            # show the QUAL controls on the configuration page; default true
 vcfDoFilter      true|false                            # show the FILTER controls; default true
 vcfDoMaf         true|false                            # show the allele frequency control; default true
 vcfDoMinAc       true|false                            # show the allele count control; default true

Other optional settings are not specific to VCF, but relevant:

@@ -235,33 +236,34 @@ phasing information of the VCF file. Each haplotype is displayed on two separate, horizontal black lines across the browser window. Each variant is drawn as a vertical dash. Homozygous variants will show two identical dashes on both haplotype lines. Phased heterozygous variants are placed on one of the haplotype lanes and unphased heterozygous variants are displayed in the area between the two haplotype lines.

Follow the steps for a normal VCF file, including moving the file to a web accessible location and generating a tabix index file, then use the following required vcfPhasedTrio trackDb settings to view the trio display:

type                   vcfPhasedTrio                 # The track type is required and must be "vcfPhasedTrio"
 bigDataUrl             http://url.to.vcfFile         # The bigDataUrl is required
 vcfChildSample         GT ID|alias                   # the Genotype column ID of the "child" sample, with an optional "|" followed by a human readable alias for the ID

There are also two optional settings for vcfPhasedTrio tracks:

There are also three optional settings for vcfPhasedTrio tracks:

vcfParentSamples       GT ID1|alias1,GT ID2|alias2        # comma separated (no spaces) list of the "parent" samples, with optional aliases
 vcfUseAltSampleNames   GT ID                              # Use the aliases in the display by default instead of the Genotype column ID
+vcfPhasedColorBy       mendelDiff|deNovo|function|noColor # allele coloring scheme, default noColor; function also requires geneTrack

Other optional settings are not specific to VCF, but relevant:

maxWindowToDraw        N                             # don't display track when viewing more than N bases
 chromosomes            chr1,chr2,...                 # track contains data only on listed reference assembly sequences

Examples

Example #1

In this example, you will create a custom track for an indexed VCF file that is already on a public server — variant calls generated by the 1000 Genomes Project. The line breaks inserted here for readability must be removed before submitting the track line:

browser position chr21:33,034,804-33,037,719
 track type=vcfTabix name="VCF Example One" description="VCF Ex. 1: 1000 Genomes phase 1 interim SNVs"
     chromosomes=chr21 maxWindowToDraw=200000