NCBI’s genome browsers and graphical sequence viewers now allow you to view BAM alignments sorted by haplotype tag. This option is useful for analyzing variants within a sequenced sample and can help you detect or validate structural variants.Figure 1. Remote BAM alignment data sorted by haplotype tag in the Genome Data Viewer. The remote BAM file was added through the “User Data and Track Hubs” feature in GDV.  You can load the remote BAM for this example through https://go.usa.gov/xpM9c. The sorted display shows that haplotype 1 contains a significant deletion in this region relative to haplotype 2 and the reference genome assembly. Aligned reads not assigned a haplotype tag in the BAM file are grouped under the heading “haplotype not set” (not shown). 

The example in Figure 1 shows BAM alignment data loaded in the Genome Data Viewer and sorted by haplotype tag.  In this case the alignments from haplotype 1 show a deletion in this region relative to haplotype 2 and the reference genome assembly.  You can explore these data further through a demonstration in the graphical sequence viewer.

As described in a previous post, you can stream your own or third-party remote BAM alignment data using the “Add Remote Files” option (Figure 1) under the User Data and Track Hubs widget in the Genome Data Viewer. Access the track display settings for a particular data track by clicking on the track title, or by using the gear icon on the right side of the track the display to sort alignments by haplotype (Figure 2).  To use this feature, your BAM file must contain reads marked with haplotype tag.Figure 2. The track display settings for the BAM alignment track showing sorting by haplotype. You can access the display settings by clicking on the track title (upper-left, circled in red).

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