874a1eb980511c7e2273d8a6e4d29f00b81eae64
braney
  Fri Sep 11 20:22:55 2026 -0700
quickLift help: list the formats that lift instead of the ones that do not, refs #35536

The "Unsupported Track Formats" section was a denylist.  It went stale as
soon as a format was added, and it was already wrong: it listed PSL and
bigChain as unsupported when both lift.

Replaced it with a "Supported Track Formats" allowlist, which matches how
the code decides.  A short paragraph after the list names the common
formats that do not lift and repeats the message the Convert page shows.
The WIG to bigWig conversion note moved out of the list into its own
paragraph.

Kept an unsupportedTypes anchor on the section so old links still land.

diff --git src/hg/htdocs/goldenPath/help/quickLift.html src/hg/htdocs/goldenPath/help/quickLift.html
index 04cbe751c94..f191ecbbbba 100755
--- src/hg/htdocs/goldenPath/help/quickLift.html
+++ src/hg/htdocs/goldenPath/help/quickLift.html
@@ -68,31 +68,31 @@
     <li>Check the <b>QuickLift tracks</b> checkbox to carry over your visible tracks,
         custom tracks, and track hubs to the target assembly. Without this checkbox, only the
         coordinate position is converted.
         <p><b>Note:</b> When a single track from a container track (such as a superTrack or
         composite) is lifted, the entire container track is carried over to the target genome
         assembly.</p>
         <div class="text-center">
         <img alt="Browser view showing QuickLift converted tracks from a different assembly" src="../../images/QuickLift/quickLiftTracks.png" width="50%">
         </div>
     </li>
     <li>Click <button>Submit</button>. The results page will show the corresponding position(s)
         in the target assembly with links to the Genome Browser. If any of your visible tracks
         use a format not supported by <span class="quicklift">QuickLift</span>, the Convert page
         will display a message: &quot;Some of your tracks failed to lift because the type is not
         supported by QuickLift.&quot; (See
-        <a href="#unsupportedTypes">Unsupported Track Formats</a> below.)
+        <a href="#supportedTypes">Supported Track Formats</a> below.)
         <p>If <span class="quicklift">QuickLift</span> was enabled, clicking a result link will
         display your lifted tracks under a green
         &quot;<span class="quicklift">QuickLift</span> from ...&quot; group in the target
         assembly. To remove <span class="quicklift">QuickLift</span> tracks, click the
         <button>Disconnect</button> button. This removes all
         <span class="quicklift">QuickLift</span> tracks from the target assembly.</p></li>
 </ol>
 
 <h3 id="visualIndicators">Visual Indicators</h3>
 <p>
 <span class="quicklift">QuickLift</span> tracks have a green left-side button bar in the Browser
 graphic (instead of the usual gray):
 </p>
 <div class="text-center">
 <img alt="Green left-side button bar indicating QuickLift tracks in the Genome Browser" src="../../images/QuickLift/quickLiftGreenbuttons.png" width="7%">
@@ -115,54 +115,62 @@
 difference.
 </p>
 <div class="text-center">
 <img alt="QuickLift Alignment Differences track showing colored triangle markers with mouseover tooltip displaying base-pair difference size and type" src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width="70%">
 </div>
 <p>
 Clicking a triangle opens a details page showing:
 </p>
 <ul>
     <li>Source and target assembly genome positions</li>
     <li>DNA sequence alignment</li>
     <li>Type and size of each alignment difference within the currently visible browser
         region</li>
 </ul>
 
-<h2 id="unsupportedTypes">Unsupported Track Formats</h2>
-<p><span class="quicklift">QuickLift</span> does not support the following track formats:</p>
+<a id="unsupportedTypes"></a>
+<h2 id="supportedTypes">Supported Track Formats</h2>
+<p><span class="quicklift">QuickLift</span> lifts the following track formats:</p>
     <ul>
-        <li>WIG &mdash; <a href="/goldenPath/help/bigWig.html" target="_blank">bigWig</a>
-            is supported; WIG tracks can be converted to bigWig using the
-            <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>wigToBigWig</code></a>
-            utility</li>
-        <li>BAM</li>
-        <li>CRAM</li>
-        <li>PSL &mdash; <a href="/FAQ/FAQformat.html#format1" target="_blank">BED</a>
-            is supported; PSL tracks can be converted to BED using the
-            <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>pslToBed</code></a>
-            utility</li>
-        <li>VCF</li>
-        <li>HIC</li>
-        <li>MAF</li>
-        <li>bigChain</li>
-        <li>Interact</li>
-        <li>narrowPeak / broadPeak &mdash;
-            <a href="/goldenPath/help/bigBed.html" target="_blank">bigBed</a>
-            is supported; since narrowPeak and broadPeak are BED-based formats, they can be
-            converted to bigBed using the
-            <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>bedToBigBed</code></a>
-            utility</li>
-        <li>pgSnp</li>
+        <li><a href="/FAQ/FAQformat.html#format1" target="_blank">BED</a> and
+            <a href="/goldenPath/help/bigBed.html" target="_blank">bigBed</a></li>
+        <li><a href="/goldenPath/help/bigWig.html" target="_blank">bigWig</a></li>
+        <li><a href="/FAQ/FAQformat.html#format9" target="_blank">genePred</a> and
+            <a href="/goldenPath/help/bigGenePred.html" target="_blank">bigGenePred</a></li>
+        <li><a href="/FAQ/FAQformat.html#format12" target="_blank">narrowPeak</a> and
+            <a href="/FAQ/FAQformat.html#format13" target="_blank">broadPeak</a></li>
+        <li><a href="/goldenPath/help/bigLolly.html" target="_blank">bigLolly</a></li>
+        <li>bigDbSnp</li>
+        <li>GVF</li>
+        <li><a href="/FAQ/FAQformat.html#format2" target="_blank">PSL</a> and
+            <a href="/goldenPath/help/bigPsl.html" target="_blank">bigPsl</a></li>
+        <li><a href="/goldenPath/help/chain.html" target="_blank">chain</a> and
+            <a href="/goldenPath/help/bigChain.html" target="_blank">bigChain</a></li>
+        <li><a href="/goldenPath/help/bigMaf.html" target="_blank">bigMaf</a> and
+            wigMaf</li>
     </ul>
+<p>
+<span class="quicklift">QuickLift</span> does not lift any other format. BAM, CRAM, VCF, HIC,
+Interact and pgSnp are among the formats it does not lift, and so are the plain MAF and net
+formats. A track in one of these formats stays in the source assembly, and the Convert page
+names the track and its format under the message &quot;Some of your tracks failed to lift
+because the type is not supported by QuickLift.&quot;
+</p>
+<p>
+A WIG track can be converted to
+<a href="/goldenPath/help/bigWig.html" target="_blank">bigWig</a> with the
+<a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>wigToBigWig</code></a>
+utility, which <span class="quicklift">QuickLift</span> does lift.
+</p>
 
 <h2 id="resources">Resources &amp; Support</h2>
 <ul>
     <li><a href="/cgi-bin/hgLiftOver" target="_blank">LiftOver</a> &mdash; convert
         coordinates or annotation files in bulk between assemblies</li>
     <li><a href="/goldenPath/help/chain.html" target="_blank">Chain format</a> &mdash;
         description of the alignment chain files used by
         <span class="quicklift">QuickLift</span> and liftOver</li>
     <li><a href="/contacts.html" target="_blank">Contact us</a> &mdash; request a new
         liftOver chain or report issues via the genome mailing list</li>
 </ul>
 
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