Reference files for PureCN pipeline

[miachom]

Hi,

I am interested in having the reference and baits files used for exome data of PureCN pipeline here https://github.com/broadinstitute/depmap_omics/blob/8e1a8b553b65b2f40ed3a8396f1a4c4275932e07/WGS_pipeline/PureCN_pipeline/README.md?plain=1#L11

How can I get access to this data? Or is this publicly available somewhere? Thank you

[5im1z]

Hi,

Interval files are public and can be found at gs://ccleparams/references/PureCN_intervals. The reference genome we use is hg38.

Best, Simone

[miachom]

@5im1z Hi Simone, sorry, but I still cannot find this link. Could you please post a functional link for these reference files?

Best, Mingkee

[5im1z]

Hi Mingkee,

If you are trying to pull it in your browser, this is the link: https://console.cloud.google.com/storage/browser/ccleparams/references/PureCN_intervals;tab=objects?prefix=&forceOnObjectsSortingFiltering=false. You might have to log in using your google credentials. Let me know if it doesn't work!

Simone

[miachom]

Hi Simone,

It works; thanks for the link!

Best, Mingkee

[miachom]

Hi Simone,

Is this reference also available publicly /Data/VCFs/Liftover/hg38.fa? I would like to get this .fa file as well and I can't seem to find it in google buckets. I tried to use our hg38 reference along with the ccle params files such as agilent_hg38_lifted_chrXY.no_header.bed and agilent_hg38_intervals.txt. But it's throwing me errors for not being able to parse.

Thanks. Mingkee

[5im1z]

Hi Mingkee,

We use gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta as our Hg38 reference fasta. If you need to pull it from the browser, you can access it through this folder which is hosted by GATK.

Thanks, Simone

[miachom]

Hi Simone,

I read in one of the announcements for mutation pipeline updates here https://forum.depmap.org/t/announcing-the-22q4-release/2125 that to run Mutect2, we don't need to use bait sets anymore. In such a case is running Mutect2 on CCLE cell lines for exome data without bait set alright? And if not, where can I find these files agilent_hg38_lifted_chrXY.no_header.bed and agilent_hg38_lifted_chrXX.no_header.bed? At the moment, I can see only for agilent hg19 and ice hg19.

Thanks for all of your responses!

Best, Mingkee

[5im1z]

Hi Mingkee,

It is correct that we are no longer using interval sets for exome mutation calls. If you need the interval files, they are stored in our public bucket gs://ccleparams where we share all of our reference files. Browser-friendly link here: https://console.cloud.google.com/storage/browser/ccleparams/references/intervals. And in case you are not aware, if you are interested in getting mutect2 calls for CCLE lines, they (among other things) can be found in our public workspace.

Simone