Best human reference genome chm13v2?

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Jacqueline Morris

• June 15, 2023 16:48

I am still seeing a lot of variant calling performed on hg38. Is the most recent T2T-CHM13 genome not the best genome to use (https://github.com/marbl/CHM13)? Is hg38 still mostly used for comparative purposes because most analyses use either hg38 or hg19?

I was planning on calling variants using the best practices for germline short variant discovery with the genome:

https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz

and ground truth variants from 1000genomes for calibration:

https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/variants/1000_Genomes_Project/chm13v2.0/

Is this not an appropriate genome/SNP set for variant calling in human? Would these be the right files?

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  SkyWarrior

  • June 17, 2023 15:03

  T2T is quite good for completeness of the genome but not ready for primetime I suppose. Many of its annotations including external databases to support variant annotation with metadata are not ready. I bet the real use of T2T and pangenome will be with mature long read technologies like Pacbio Revio data and Illumina long read. 

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