How to align short reads to repetitive regions
I have aligned paired-end 100bp short reads to a reference genome using bwa-mem with no extra options.
When inspecting the alignment in IGV I notice gaps where I believe should be the locations of Short Tandem Repeats.
The end goal is to use this alignment to call genotypes on Short Tandem Repeats but this fails without informative reads (reads spanning, flanking or enclosing the repeat).
How do I allow bwa-mem to align reads to these regions?
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