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hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Apache License 2.0
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Potential source of validated somatic mutations #387

Open hammer opened 8 years ago

hammer commented 8 years ago

A recent Nature article on pancreatic cancer sequenced 382 patients from the Australian Pancreatic Cancer Genome Initiative (APGI) and found 23,538 high confidence coding mutations, of which, 7,377 were verified using orthogonal approaches. The data appears to be available from the ICGC data portal at https://dcc.icgc.org/projects/PACA-AU. We should see if we can get BAMs or FASTQs for the patients that have validated mutations!

arahuja commented 8 years ago

Another option is http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151664

I've contacted the authors for access to the data as there were no details with the paper, hopefully this will be easier to obtain than the pancreatic set.

hammer commented 8 years ago

Another option: http://txcrb.org/open.html