CCLE mutaitons/CNV bed files for WES data analysis

Q&A
1

Hi Depmap team,

Can you please point me to the targets bed files used to call mutation or CNV using WES bam files available via ftp ?

Thanks in advance…

2

Can someone help us with bed files to use for variant or CNV calling ?

3

Hi!

Can you clarify what you mean by bed files? Are you referring to the interval files for our WES data? If so, maybe this post answers your question.
Let me know if you have any other questions!

Best,
Simone

4

Hi, Thanks for the details Simz. That was exactly I’m looking for…

Is there anyway to get the information on which target intervals (Agilent vs ICE) are used for each celllline ?

5

Hi,

Unfortunately there isn’t a way to get that information on the portal now, but it’s something we are currently working on as part of the effort to improve our metadata sharing. Please stay tuned for the next release!

Best,
Simone

1 Like
6

How can I download the FASTQ or Bam & Bam.bai file from illumina RNA-seq for CRC cell lines so that we can analyse further in IGV ?

7

Hi,

Please see this post for details on how to access our bam data.

Best,
Simone