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mahulchak / svmu

A program to call variants from genome alignment
GNU General Public License v3.0
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Does SVMU work with human genome? thanks #5

Closed JiguangPeng closed 4 years ago

mahulchak commented 6 years ago

I have not tested it on human genome. You can run it and see. you could also try to repeatmask your genome before running svmu on it. There are some issues with highly heterozygous or highly repetitive genomes like maize. I am working on some updates to mitigate them.

JiguangPeng commented 6 years ago

I have read the method of the your nature paper. when should we use mgaps to cluster maximal exact matches before svmu? which is not described here.

mahulchak commented 6 years ago

That's the older version. You can find that pipeline here: https://github.com/mahulchak/svmu/tree/v0.1beta

On Thu, Apr 19, 2018 at 6:04 AM 神说要有光 notifications@github.com wrote:

I have read the method of the your nature paper. when should we use mgaps to cluster maximal exact matches before svmu? which is not described here.

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JiguangPeng commented 6 years ago

thank you for the reply. I will try that