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Dear all,
in my lab we are using the Nextera Rapid Capture Exome kit to do whole exome sequencing. Until now I have used GRCh37 as a reference for alignment and variant calling. However, now that the new ref GRCh38 has been released over three years ago and support (e.g. software and data files) are now more widely available for GRCh38, I would like to switch the reference to take advantage of the new developments.
However, the Nextera kit was designed based on GRCh37 and I am uncertain what the effect of a switch of reference would be. I asked this question to Illumina tech support, but they do not know. Do you think it is a good idea to use GRCh38 as reference? I imagine that for the parts of the reference that stayed the same there will be no difference. GRCh38 certainly has some novelties like alternate contigs, and I'm not quite sure what the effect will be there.
Any comments are appreciated. Has somebody aligned Nextera reads to GRCh38 already?
in my lab we are using the Nextera Rapid Capture Exome kit to do whole exome sequencing. Until now I have used GRCh37 as a reference for alignment and variant calling. However, now that the new ref GRCh38 has been released over three years ago and support (e.g. software and data files) are now more widely available for GRCh38, I would like to switch the reference to take advantage of the new developments.
However, the Nextera kit was designed based on GRCh37 and I am uncertain what the effect of a switch of reference would be. I asked this question to Illumina tech support, but they do not know. Do you think it is a good idea to use GRCh38 as reference? I imagine that for the parts of the reference that stayed the same there will be no difference. GRCh38 certainly has some novelties like alternate contigs, and I'm not quite sure what the effect will be there.
Any comments are appreciated. Has somebody aligned Nextera reads to GRCh38 already?