GRCh37-lite and GRCh37

[Avali, Vijayalakshmi Raghu]

Hi,

 

We are working with some TCGA dataset that is based on GRCh37-lite. We have to compare the results to another dataset that is based on GRCh37. When we compared the two reference sequences, we found that  the fasta sequence for chromosome 6 differ in these two genome builds (GRCh37 and GRCh37-lite). Do you have the file for converting from GRCh37-lite to GRCh37?  If so, will you provide it to us?

 

Thank you.

 

Best regards,

Viji Avali

[Cath Tyner]

Hello Viji,

Thank you for inquiring regarding the chrom 6 GRCh37-lite to GRCh37 differences and potential alignment files. 

We do not have any alignment mapping files among those particular assemblies. 

One of our engineers has noted that chrom 6 does not appear to be different among GRCh37-lite to GRCh37. 

As noted from:

ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/README.GRCh37-lite

"GRCh37-lite is a subset of the full GRCh37 human genome assembly (assembly

accession GCA_000001405.1) plus the human mitochondrial genome reference

sequence (the "rCRS") from Mitomap.org. This set of sequences excludes all the

alternate loci scaffolds of the full GRCh37 assembly, and has the

pseudo-autosomal regions (PARs) on chromosome Y masked with Ns. This haploid

representation of the genome is provided as a convenience for use in alignment

pipelines that cannot handle the multiple placements expected in the PARs and

in regions of the genome that are represented by the alternate loci."

Since UCSC did not generate these assemblies, I can't guarantee that we can provide further information, but you are welcome to respond and describe the differences you are seeing in greater detail.

Meanwhile, you may be able to find better answers to your questions by contacting the NCBI Helpdesk

​.​

​I believe I've seen someone on the Biostars forum who may have done something similar, so it might be worthwhile to post your question there as well. ​

You might also try contacting TCGA for help.

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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