b4354dab1ce9929f4cd6b81628b545a3b0bd9840 dschmelt Wed Feb 26 14:43:22 2020 -0800 Adding note about bigDataIndex keyword #25018 diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html index fe119c1..2db24c4 100755 --- src/hg/htdocs/goldenPath/help/vcf.html +++ src/hg/htdocs/goldenPath/help/vcf.html @@ -39,31 +39,37 @@
  • Create VCF or convert another format to VCF. Items must be sorted by genomic position.
  • Compress your .vcf file using the bgzip program: 
    bgzip my.vcf
    For more information about the bgzip command, run it with no arguments to display the usage message.
  • Create a tabix index file for the bgzip-compressed VCF (.vcf.gz): 
    tabix -p vcf my.vcf.gz
    The tabix command appends .tbi to the my.vcf.gz filename, creating a binary index file named my.vcf.gz.tbi with which genomic coordinates can quickly be translated into file offsets in my.vcf.gz.
  • Move both the compressed VCF file (my.vcf.gz) and tabix index file - (my.vcf.gz.tbi) to an http, https, or ftp location.
    • + (my.vcf.gz.tbi) to an http, https, or ftp location.Note that the Genome Browser + looks for an index file with the same URL as the VCF file with the .tbi suffix added. If your + hosting site does not use the filename as the URL link, you will have to specifically + call the location of this .vcf.tbi index file with the bigDataIndex keyword. + This keyword is relevant for Custom Tracks and Track Hubs. You can read more about + bigDataIndex in + the TrackDb Database Definition page.
  • Construct a custom track using a single track line. The basic version of the track line will look something like this: 
    track type=vcfTabix name="My VCF" bigDataUrl=http://myorg.edu/mylab/my.vcf.gz
    Again, in addition to http://myorg.edu/mylab/my.vcf.gz, the associated index file http://myorg.edu/mylab/my.vcf.gz.tbi must also be available at the same location.
  • 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