Access to WGS VCF for OCI-LY18 (ACH-001616 / CDS-T3gUBN)

Q&A
1

OmicsProfiles lists WGS profile PR-olxzDg for ACH-001616 (OCI-LY18), sequencing ID CDS-T3gUBN, dated 2024-05-21. However, CDS-T3gUBN is absent from the public depmap-omics-ccle AWS WGS VCF/CRAM inventory and from the CCLE_v2 Terra sample table. Is the Mutect2 WGS VCF or CRAM for CDS-T3gUBN publicly accessible, and if so, where can it be downloaded?

2

Hi,

The public AWS and terra workspaces only contain data from cell lines published in the CCLE2 paper. Since this publication, DepMap has expanded to include many more non-CCLE cell lines, OCI-LY18 being one of them. Genomic data for non-CCLE cell lines can be accessed on dbGaP. Please see our resource page for more details.

Simone

3

Thanks, Simone. I located the DepMap dbGaP study, phs003444.v3.p1.

Before initiating a controlled-access request, could you confirm whether OCI-LY18 (ACH-001616), specifically WGS sequencing ID CDS-T3gUBN, is included in the current release?

Also, does the dataset include the genome-wide Mutect2 VCF files, or only FASTQ/CRAM files? We are hoping to analyze indel mutational signatures using the existing variant calls.

Many thanks!

4

Hi,

Looks like for ACH-001616, only the RNA and WES sequencing files are available on dbGaP at the moment. WGS has been submitted and will be available as part of our v4 dataset which will be live later this year. Unfortunately we do not provide VCF files on dbGaP, only bam/cram files.

Thanks,

Simone