Looking for VCF files of CCLE mutation data

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.

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.

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.

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):

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

Hi @jnoorbak ,

I could find the b37 reference file:

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.

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