Cosmic track in IGV

[northwestwitch]

From the notes of the last user meeting (#1679)

[northwestwitch]

I'll give this one a try!

[northwestwitch]

I've been starting working on this and so far I've figured out that the tracks can be showed as: cosmic coding variants and cosmic non coding variants.

Both can be imported as VCF files from cosmic: https://cancer.sanger.ac.uk/cosmic/download (VCF Files (coding and non-coding mutations). NOTE that default VCFs are annotated in build 38.

The links don't work out of the box because:

• One needs to login before downloading them
• An index must be created

What should be done:

• Download the same variants but annotated with HG19
• Create an index for all of them
• Upload everything on a cloud bucket (I do have one so we can use that)
• Create an access policy to reach the files from Scout (because of cosmic licensing the files can't be public)

Looks a bit complicated but I think I can manage!