Comments (8)
Hi Simone,
It works; thanks for the link!
Best,
Mingkee
from depmap_omics.
Hi,
Interval files are public and can be found at gs://ccleparams/references/PureCN_intervals. The reference genome we use is hg38.
Best,
Simone
from depmap_omics.
@5im1z
Hi Simone, sorry, but I still cannot find this link. Could you please post a functional link for these reference files?
Best,
Mingkee
from depmap_omics.
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
from depmap_omics.
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
from depmap_omics.
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
from depmap_omics.
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
from depmap_omics.
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
from depmap_omics.
Related Issues (20)
- PureCN double counting minor allele freq
- add timestamped CIVIC db
- update mutation mapping to entrez
- automate STR inference + gumbo import in fingerprinting
- add cosmic actionability annotation to open cravat
- Arm-level CNA and aneuploidy score
- Generate RNAseq effective length matrix
- New cell lines in 23q2 release not at Cellosaurus (no RRID) HOT 1
- mask segmental duplication and repeat masker regions
- add quality filter and segdup/rm masking to merged mutation pipeline
- Availability of PureCN copy number calls for DepMap 23Q2 HOT 1
- refactor vcf_to_depmap that is compatible with latest MAF format HOT 2
- Duplicate RNA-seq omics profiles for cell lines HOT 2
- Convert the WGS_CCLE jupyter notebook into command line in the future
- creating mutation matrices too slow
- use mutation rescue list to un-mask cn genes
- add hotspot as a column in mutation table
- move TERT mutation rescue from postprocessing to vcf_to_depmap
- debug: cn postprocessing function blists wrong seq entries
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