has gatk consider Duke regions and CRG36mer

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that girl

• June 19, 2020 03:39

Dear professor,

has gatk considered the poorly mappable region in genome. which is Duke regions and CRG36mer.

I just read a paper and it refered to this, but I do not know what it is , I also tried to find many other papers, but failed . so ask for help here.

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  that girl

  • June 20, 2020 14:17

  any response, thanks 

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  David Benjamin

  • June 21, 2020 05:43

  GATK tools account for mapping error.  There are many definitions of mappability, most of which are reasonable.  I'm not familiar with the Duke regions but I can guess that the CRG36mer mappability of a region is related to the uniqueness (or the extent of non-uniqueness) of its 36-mers.  Given that sequencing reads these days are hardly ever smaller than 75 bases, this would not be an appropriate mappability to use.  Furthermore, paired-end reads are much more mappable than single-end reads so one much be careful about kmer mappability scores.

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