Visualizing the DRAGEN Evidence BAM in Integrative Genomics Viewer (IGV)
The DRAGEN small variant caller is a haplotype-based caller which performs local assembly of all reads in an active region into a de Bruijn graph (DBG). The assembly and realignment step (using pair-HMM) performed by variant caller aims to correct mapping errors made by the original aligner and improves the overall variant caller accuracy. Using the evidence BAM, we can view how the variant caller sees the read evidence and how the reads have been realigned making it a very useful debugging tool. More information about the DRAGEN Small Variant Caller algorithm can be found in the user guide.
By default, the evidence BAM contains only a subset of regions processed by the small variant caller. Only regions which have candidate indel variants and some percentage of soft-clip reads in the pile up are realigned and output in the evidence BAM. This is done to reduce the run time overhead needed to generate the evidence BAM. Realigned reads, badly mated reads (when the read and its mate are mapped to different chromosomes) and reads disqualified by the variant caller based on the read likelihood scores are included in the evidence BAM.
Disqualified reads are tagged with the DQ tag while Badly Mated reads are tagged with the BM tag. The Alignment score tag AS is forced to be 0 for such reads in the evidence BAM and hence can be filtered from the IGV pile up by setting the minimum AS score to be 1. This can be changed from the Preferences dialog box which can be accessed from the View menu.
DRAGEN outputs all haplotypes, constructed from the de Brujin graph, in the evidence BAM as single reads covering the entire active region if the '--vc-evidence-bam-output-haplotypes true' (default: false) tag is included in the DRAGEN command. These haplotypes are named Haplotype 0, Haplotype 1 and so on. The haplotypes and reads are tagged with different read groups, and the 'Color Alignments By' > read group or 'Group Alignments By' > read group option can be used to separate the two (can access these options by right clicking on the alignment track).The haplotypes are tagged with read group EvidenceHaplotype and the reads are part of the EvidenceRead_Normal/Tumor read group.
For instance, the alignments below were grouped and colored by Read Group.
Haplotypes and the reads that uniquely match with each of them based on read likelihood calculations share a common 'HC' tag. Hence, the "Color Alignments By > Tag > HC" option can be used to identify the haplotypes the reads map to. Reads that match more than one haplotype well do not have an HC tag.
For instance, red-colored reads in the 'EvidenceRead_Normal' match the first haplotype in the EvidenceHaplotype section (Haplotype 0; HC=0) while the blue-colored reads match to the second haplotype (Haplotype 1; HC = 1).
This can give a user an estimate of read support for different candidate haplotypes. More information about the Evidence BAM generated by DRAGEN can be found in the user guide.
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