Question: Can sciclone handle multiallelic variants?
1
gravatar for sm.hashemin
6 months ago by
sm.hashemin60
sm.hashemin60 wrote:

Dear people I was wondering if sciclone could handel multialllic variants.

sofar I am filtering them out because it needs more than three column.

on idea would be write them under another, like : chrom1 pos1 A G chrom1 pos1 A C chrom1 pos2 ref var

But preferably I would like to calculate MAF based on var count of all kinds of variant calls. Just in case if sciclone could not handel the multiallelic variants.

Best

ADD COMMENTlink modified 6 months ago by Chris Miller20k • written 6 months ago by sm.hashemin60

Tagging: Chris Miller

ADD REPLYlink written 6 months ago by genomax59k
1
gravatar for Chris Miller
6 months ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Sciclone was written to assume that each variant's chr:pos would be unique. The simple workaround for collisions like this is just to give the second variant a different chrom and pos. (i.e. chr99 999999999). The places actual coordinates are used are for matching up variants with the CN regions to exclude non-CN neutral sites. It will also be output that way in the results, but again, it's an easy fix to change it back.

If anyone wanted to hack on the code to add support, it wouldn't be that difficult to implement, but it's not a priority for me at the moment. (pull requests welcome!)

ADD COMMENTlink written 6 months ago by Chris Miller20k
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