Can sciclone handle multiallelic variants?
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3.2 years ago
sm.hashemin ▴ 90

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

sciclone multiallelic_variants • 632 views
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Tagging: Chris Miller

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3.2 years ago

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!)

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