SVs, noncoding mutations for CCLE data

[Xiaolong_Cao]

Any plans for additional WGS data?

We have released several WGS in 21Q1 and moving forward there will be more WGS instead of WES. At the moment we haven’t had the bandwidth to provide derivatives of this data such as SVs, noncoding mutations, etc. But we plan to generate a subset of WGS derivatives in the future. DepMap is in the process of submitting samples to dbGaP for regular upload to SRA (or possibly GDC) but the process is quite lengthy. So at the moment we do not have a projection on when the WGS bam files will be availa…

in studies generating new gene models like this one Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer | Genome Biology | Full Text (biomedcentral.com)

We may need non-coding variants to analyze neoantigens. I am wondering is it possible to provide the vcf file or some more variants, which will be very helpful for researchers. Otherwise we need to run the variant call locally, which can be much more challenging.

The files can be gzipped which will greatly reduce the file sizes and save the bandwidth.
Thank you！

[simz]

Hi,

Thanks for reaching out. In fact we do provide unfiltered mutect2 VCFs through our Terra workspace under the column name “mutect2_vcf_wgs”. Please see this post for details on how to access this data.

Thanks,
Simone