vcf

lidaof · May 4, 2021 · e74de70 · e74de70
1 parent f44bed3
commit e74de70
Show file tree

Hide file tree

Showing 3 changed files with 15 additions and 0 deletions.
diff --git a/docs/_static/vcf1.png b/docs/_static/vcf1.png
diff --git a/docs/_static/vcf2.png b/docs/_static/vcf2.png
diff --git a/docs/tracks.rst b/docs/tracks.rst
@@ -268,6 +268,21 @@ The bed file like above can be convert to bigbed format using the commands below
     bedSort peaks_rgb.bed peaks_rgb.bed
     bedToBigBed peaks_rgb.bed hg38.chroms.sizes peaks_rgb.bigbed
 
+Variant Tracks
+--------------
+
+VCF
+~~~
+
+``VCF`` files can be visulaized in the browser for displaying variant call data. Currently VCF file need to be bgzip and tabix indexed for submission.
+When viewing a ``VCF`` track at a region greater than 100Kb, the track will be displayed as numerical track showing the density of the variant calls. When view region is less than or equal to 100Kb, it will be displayed in Full mode.
+Click each of the variant item will show the popup tooltip with more information about this variant. 
+
+.. image:: _static/vcf1.png
+
+Color of each variant item are encoded based on the quality value, color of high  and low quality variant can be customized from right clicking menu.
+
+.. image:: _static/vcf2.png
 
 Numerical Tracks
 ----------------