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BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of nucleotide sequence alignments. Many next-generation sequencing and analysis tools work with SAM/BAM. For custom track display, the main advantage of indexed BAM over PSL and other human-readable alignment formats is that only the portions of the files needed to display a particular region are transferred to UCSC. This makes it possible to display alignments from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC. Both the BAM file and its associated index file remain on your web-accessible server (http, https, or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed up interactive display. If you do not have access to a web-accessible server and need hosting space for your BAM files, please see the Hosting section of the Track Hub Help documentation.
The typical workflow for generating a BAM custom track is this:
samtoolswith no command line arguments; it should print a brief usage message. For help with
samtools, please contact the SAM tools mailing list.
If converting a SAM file that does not have a proper header, the
samtools view -S -b -o my.bam my.sam
-Toption is necessary. For more information about the command, run
samtools viewwith no other arguments.
The sort command appends
samtools sort my.bam my.sorted samtools index my.sorted.bam
my.sorted, creating a BAM file of alignments ordered by leftmost position on the reference assembly. The index command generates a new file,
my.sorted.bam.bai, with which genomic coordinates can quickly be translated into file offsets in
my.sorted.bam.bai) to an http, https, or ftp location. Note that the Genome Browser looks for an index file with the same URL as the BAM file with the .bai 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 .bam.bai index file with the
bigDataIndexkeyword. This keyword is relevant in Custom Tracks and Track Hubs. You can read more about bigDataIndex in the TrackDb Database Definition page.
Again, in addition to http://myorg.edu/mylab/my.sorted.bam, the associated index file http://myorg.edu/mylab/my.sorted.bam.bai must also be available at the same location. If not, you can specify the URL with the
track type=bam name="My BAM" bigDataUrl=http://myorg.edu/mylab/my.sorted.bam
All options are placed in a single line separated by spaces. In the example below, the lines are broken only for readability. If you copy/paste this example, you must remove the line breaks. Click here for a text version that you can paste without editing.
track type=bam bigDataUrl=http://... pairEndsByName=. pairSearchRange=N bamColorMode=strand|gray|tag|off bamGrayMode=aliQual|baseQual|unpaired bamColorTag=XX minAliQual=N showNames=on|off name=track_label description=center_label visibility=display_mode priority=priority db=db maxWindowToDraw=N chromosomes=chr1,chr2,...
The track type and bigDataUrl are REQUIRED:
The remaining settings are OPTIONAL. Some are specific to BAM:
Other optional settings are not specific to BAM, but relevant:
pairEndsByName any value # presence indicates paired-end alignments pairSearchRange N # max distance between paired alignments, default 20,000 bases bamColorMode strand|gray|tag|off # coloring method, default is strand bamGrayMode aliQual|baseQual|unpaired # grayscale metric, default is aliQual bamColorTag XX # optional tag for RGB color, default is "YC" minAliQual N # display only items with alignment quality at least N, default 0 showNames on|off # if off, don't display query names, default is on
name track label # default is "User Track" description center label # default is "User Supplied Track" visibility squish|pack|full|dense|hide # default is hide (will also take numeric values 4|3|2|1|0) bigDataUrl https://your.bam.bai.com # default is the bigDataUrl with .bai added to the end priority N # default is 100 db genome database # e.g. hg18 for Human Mar. 2006 maxWindowToDraw N # don't display track when viewing more than N bases chromosomes chr1,chr2,... # track contains data only on listed reference assembly sequences doWiggle on|off # if on, show data as density graph, default is off
The BAM track configuration help page describes
the BAM track configuration page options corresponding to
bamColorTag in more detail.
pairSearchRange applies only when
pairEndsByName is given. It allows for
a tradeoff of display speed vs. completeness of pairing the paired-end alignments. When paired ends
are split or separated by large gaps or introns, but one is viewing a small genomic region, it is
necessary to search a large number of bases upstream and downstream of the viewed region in order
to find mates of the alignments in the viewed region. However, searching a very large region can be
slow, especially when the alignments have deep coverage of the genome. To ensure that all properly
paired mates will be found,
pairSearchRange should be set to the largest genomic size
of a mapped pair. However, it can be set to a smaller size if necessary to speed up the display, at
the cost of some items being displayed as unpaired when the mate is too far outside the viewed
In this example, you will create a custom track for an indexed BAM file that is already on a public server — alignments of sequence generated by the 1000 Genomes Project.
You can paste the URL
directly into the custom track management page
for the human assembly hg18 (May 2006), then press the submit button. On the following
page, press the chr21 link in the custom track and navigate to position
chr21:33,038,946-33,039,092 to see the reads in the new BAM track.
Alternatively, you can specify more visualization options by creating a "track" line. The line breaks inserted here for readability must be removed before submitting the track line:
track type=bam name="BAM Example One" description="Bam Ex. 1: 1000 Genomes read alignments (individual NA12878)" pairEndsByName=. pairSearchRange=10000 chromosomes=chr21 bamColorMode=gray maxWindowToDraw=200000 db=hg18 visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam
Include the following "browser" line to view a small region of chromosome 21 with alignments from the .bam file:
browser position chr21:33,038,946-33,039,092
Note if you copy/paste the above example, you must remove the line breaks (or, click here for a text version that you can paste without editing).
Paste the "browser" line and "track" line into the custom track management page for the human assembly hg18 (May 2006), then press the "submit" button. On the following page, press the chr21 link in the custom track listing to view the BAM track in the Genome Browser.
In this example, you will create indexed BAM from an existing SAM file. First, save this SAM file
samExample.sam to your machine. Perform steps
1 and 3-7 in the workflow described above, but substituting
my.sam. On the custom track management
page, click the "add custom tracks" button if necessary and make sure that the genome
is set to Human and the assembly is set to Mar. 2006 (hg18) before pasting the track line and
submitting. This track line is a little nicer than the one shown in step 6, but remember to remove
the line breaks that have been added to the track line for readability (or, click
here for a text version that you can paste without
track type=bam name="BAM Example Two" bigDataUrl=http://myorg.edu/mylab/my.sorted.bam description="Bam Ex. 2: Simulated RNA-seq read alignments" visibility=squish db=hg18 chromosomes=chr21 browser position chr21:33,037,317-33,038,137 browser pack mrna
If you would like to share your BAM data track with a colleague, learn how to create a sharable URL by looking at this page.