Looking for VCF files of CCLE mutation data

Q&A
1

Hello DepMap team,
I wonder if VCF files of CCLE mutation data are accessible from DepMap or CCLE’s data portals or from somewhere else.

In addition to the table available from DepMap’s portal (CCLE_mutations.csv), I could only find the mutations in the MAF format are available from CCLE’s website (https://portals.broadinstitute.org/ccle/data) and the raw data (BAM files) that is available from SRA (PRJNA523380).

Could you please let me know if CCLE’s VCF files are accessible?
Thank you.

2

Thanks for your question. Currently we do not provide raw VCF files, but may add more fields to the CCLE_mutations.csv in the future.

3

Thank you very much for the reply @jnoorbak . I will look forward to the future releases for the details about the mutations. :+1:

I have one related question. Until the details of the mutations are released, I wonder if it would be possible to map the genome coordinates from the CCLE_mutations.csv file onto a genome assembly to get more insights into the mutations of interest?
As far I know, those coordinates correspond to GRCh37 assembly. But I am not sure which reference file I should be using to correctly map the coordinates. For example, do they correspond to the Ensembl assembly or Broad’s assembly. I wonder if there are any suggestions regarding this.
Thank you.

4

Hi, I believe that for the regular chromosomes (1-22, XY) this doesn’t matter. But you can download the reference file from here (on google cloud):
gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta

To the best of my knowledge this reference file is b37. Please check this link for more information.

5

Hi @jnoorbak ,

I could find the b37 reference file:
https://console.cloud.google.com/storage/browser/_details/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta

However, I couldn’t open this link: gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta
I hope these are the same files.

Thank you very much for the answer.

6

The path I provided was GCS path. The HTTPS version can be accessed through this link:

https://console.cloud.google.com/storage/browser/_details/firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta