Question: Current version of human reference Genome Assembly
gravatar for kspata
2.1 years ago by
kspata70 wrote:


I wish to perform variant analysis for exon capture data. The samples are human tissue samples. I already have the sequencing data and the list of exons to analyze. The exon co-ordinates are taken from the GCF_000001405.38 assembly.

I looked up on the UCSC genome browser and there the hg38 assembly version is GCA_000001405.15. So I looked up on NCBI and found this link to the latest version of the assembly.


In this, I have downloaded the GCF_000001405.38_GRCh38.p12_genomic.fna.gz file. Is this the correct reference or should I use the one on UCSC genome browser?

UCSC Genome Browser

I will appreciate the guidance.


reference assembly genome • 1.1k views
ADD COMMENTlink modified 2.1 years ago by vkkodali2.2k • written 2.1 years ago by kspata70

See the blog post from Heng Li and Which human reference genome should I use?

ADD REPLYlink written 2.1 years ago by WouterDeCoster44k
gravatar for vkkodali
2.1 years ago by
United States
vkkodali2.2k wrote:

GCA_000001405.15 and GCF_000001405.26 are identical. They are GRCh38 without any patches. Here's an explanation about patches from GRC: GCF_000001405.38 is the latest version of GRCh38 with patches. Depending on your use case, you may not need the assembly with the latest patches. In such a situation, you can use GRCh38 without any patches (GCF_000001405.26) from here:

ADD COMMENTlink written 2.1 years ago by vkkodali2.2k
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