Open preprint reviews by Hugues Sicotte

UPS-indel: A Universal Positioning System For Indels

Mohammad Shabbir Hasan, Xiaowei Wu, Layne T. Watson, Zhiyi Li, Liqing Zhang

Review posted on 09th June 2017

Good and bad points, but can't use it as is.

Good:

The Table 5 example (splitting of alleles of indels) is a warranted improvement, especially since the VCF spec states that the alt-alleles do not all have to be included in the genotypes.. so sharing a subset of alleles is cause enough to merge.

Bad:
However,the Horizontal decomposition (Table 6) violates the principle that the two sequences (after indels) should be identical.(Check the genome browser). Because the variants are nearby, you can choose to merge the alleles, but there is no evidence that these variants are not independent.. so that is not warranted.

I downloaded the tool and there is no option to turn off horizontal decomposition.

Also, the other operation I really want is merge to VCF (with genotypes) and this tool doesn't do that and it can get a little complicated to figure out.

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