Jeff Hammerbacher

Potential source of validated somatic mutations

2

A recent Nature [article](http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16965.html) 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...

It would be nice to have a sample report with annotations to guide readers

Using e.g. fusioncatcher or [ChimPipe](http://biorxiv.org/content/early/2016/08/22/070888)

Make a public bucket or NFS filer available w/ sample data

4

It would be nice for potential users to be able to run the pipeline against some sample input and output data to confirm they're running a pipeline correctly.

Document command-line args required by pipeline COMMAND

1

When I run `KETREW_CONFIG=./ketrewdocker/configuration.ml ocaml jh-epidisco.ml pipeline --help` I am greeted with a wonderful list of arguments; given a `stratotemplate` setup, could we also document some good default values for...

Need to install dot?

1

I haven't dug into whether this error message matters yet but the `stderr` for my epidisco run said > /nfswork/biokepi/ketrew-host-playground/ketrew_2016-08-09-08h19m23s345ms-UTC_759304190/monitored_script: line 837: dot: command not found > chmod: changing permissions...

Make it easy to see what has changed when clinical data is updated

1

Feature request from @jburos

Deprecate links to IGV

1

We should use this issue to catalogue IGV features missing from pileup.js

Cf. #800; may be possible now with https://bvaughn.github.io/react-virtualized/?