Question: Structural Variation data of ICGC/PCAWG: 2,658 cancers across 38 tumour types
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gravatar for Shicheng Guo
5 days ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Hi All,

Anyone has download structural Variation data of ICGC/PCAWG: 2,658 cancers across 38 tumor types? I am very confused that I have download several different version of these data, but none of them have 2658 samples? I am wondering anyone tried to download ICGC data? and whether the samples are same as the paper claimed?

https://www.nature.com/articles/s41586-019-1913-9#Sec2

Thanks.

Shicheng

pcawg icgc • 41 views
ADD COMMENTlink modified 5 days ago by d-cameron2.2k • written 5 days ago by Shicheng Guo8.3k
2
gravatar for d-cameron
5 days ago by
d-cameron2.2k
Australia
d-cameron2.2k wrote:

I've been using the calls from the PCAWG final public release:

https://dcc.icgc.org/releases/PCAWG/consensus_sv

https://dcc.icgc.org/releases/PCAWG/consensus_cnv

At 2749 SV call sets and 2778 CNV call sets across ICGC and TCGA, that's more than the claimed 2,658 and means some samples are missing SV calls. I haven't reconciled these against the 2,658 samples to determine the extent of the overlap.

ADD COMMENTlink written 5 days ago by d-cameron2.2k
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