I think it would be useful to calculate a metric for the proportion/number of clipped reads per contig position. Is there currently a way to do this or can you suggest how I might go about doing this?
Assemblers which can't handle high levels of heterozygosity often clip many reads back to the same position and this hides the true level of heterozygosity. Being able to see where the number of clipped reads suddenly jumps up would be a signature for highly heterozygous loci.
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