GRCh38_verily vs GRCh38

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Damian Loska

• June 01, 2020 11:45

Hi,

Which reference should I use for my analyses? 

The reference "GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz" (GRCh38_verily) from https://cloud.google.com/life-sciences/docs/resources/public-datasets/reference-genomes seems to be reasonable but all pipelines from Terra/GATK refers to the "original" GRCh38.

Will it be a big "faux pa" if I use "GRCh38_verily" instead of the "original" one? Will I have problems in downstream analyses? 

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  danilovkiri

  • June 01, 2020 18:22

  Hi Damian Loska

  No, you will not have any problems. The Verily's build is described here (https://cloud.google.com/life-sciences/docs/resources/public-datasets/reference-genomes) with all the differences explicitly stated. Note that it has chrN-like contig naming scheme, thus you have to maintain it for every external resource VCF you intend to use in your pipeline.

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