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Question: Varscan unable to compare somatic with germline samples
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gravatar for a.januszewski
7 months ago by
a.januszewski • 10
a.januszewski • 10 wrote:

Hi,

I am trying to compare tumour with normal to call variants in varscan. I dont seem able to do this and understand it may be related to the version on usegalaxy. Is this the case? (and if it is will it be updated?)

If not what approach should I use to filter germline variants in somatic variant calling?

Thanks

Adam
somatic variant varscan cancer usegalaxy.eu • 305 views
ADD COMMENT • link •
modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by a.januszewski • 10
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gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the version of Varscan at Galaxy Main https://usegalaxy.org is the older version. There is a newer version in the ToolShed, but it does not include the somatic function either. I am not sure if there are plans to update the tool or not, but have asked one of the tool authors at Gitter, please follow along and join in if you'd like to: https://gitter.im/galaxy-iuc/iuc?at=5acfd29d6bbe1d2739de622d

Thanks! Jen, Galaxy team
ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

Update: I found the updated tools at Galaxy Europe https://usegalaxy.eu. Try working there instead for this functionality. The function was not added to the original baseline Varscan tool but is captured in other variants of the tool. Find these by searching in the tool panel with the keyword "varscan".

Thanks!

ADD REPLY • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks a lot - that is very helpful.

bw

Adam

ADD REPLY • link written 7 months ago by a.januszewski • 10
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