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Old 01-14-2014, 11:51 AM   #1
Location: San Francisco

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Cool Not a Big Deal, GRCh38: A Semi-Casual Comparison of the New Human Reference Genome

Over christmas GRCh38, the newest human reference genome assembly, was released.Internally we have been using chromosome 20 of human reference builds to benchmark tools and pipelines with datasets. A BWA sequence alignment of the same dataset, generated on a HiSeq 2500, across the last major release GRCh37.69 and the new GRCh38 was performed.

Quantifiably, GRCh38 is very similar to the later GRCh37 releases, showing a change rate of 1 change every 159,558 bases on 37.69 and 1 change every 156,779 bases on 38 for our chromosome 20 dataset.Ts/Tv ratios between the two alignments of the same data across the two references to be quite similar at 0.3527 and 0.3445, respectively. Back of the envelope math seems to give a Δ of +19,359 between GRCh37.69 and 38.
Annotations have a large deviation, to be expected for now.

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Last edited by FractalExpression; 01-15-2014 at 03:50 PM. Reason: one more figure
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Old 02-07-2014, 09:34 AM   #2
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A BWA sequence alignment
Do you think this an appropriate aligner to use to fully take advantage of the new reference genome given its structure?

It seems incorrect to take a tool optimized for the linear GRCh37, apply it to the graph GRCh38, and then state that the difference between 38 and 37 is "not a big deal".
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Old 02-07-2014, 09:43 AM   #3
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Discussing the primary assemblies themselves, that is not to include alternate regions available for 38, BWA is an appropriate choice- the aligner isn't necessarily trained for GRCh37.

But you're right, how best to utilize the alternate regions, and updating current aligners to take advantage of that is a different question than a quick comparison for anyone considering a primary assembly remap of their data.
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grch38, human reference quality, remap, sequence alignment, visualization

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