Question: Current version of human reference Genome Assembly
0
gravatar for kspata
7 months ago by
kspata50
Chicago
kspata50 wrote:

Hi,

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.

GRCh38.p12

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.

Thanks!!!

reference assembly genome • 462 views
ADD COMMENTlink modified 7 months ago by vkkodali1.1k • written 7 months ago by kspata50
2

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

ADD REPLYlink written 7 months ago by WouterDeCoster39k
2
gravatar for vkkodali
7 months ago by
vkkodali1.1k
United States
vkkodali1.1k wrote:

GCA_000001405.15 and GCF_000001405.26 are identical. They are GRCh38 without any patches. Here's an explanation about patches from GRC: https://www.ncbi.nlm.nih.gov/grc/help/patches/ 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: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38/GCF_000001405.26_GRCh38_genomic.fna.gz

ADD COMMENTlink written 7 months ago by vkkodali1.1k
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