Support with Mutect

[Loke Kok Keong]

Hi,

    Would like to know why Seqmule not incorporate Mutect? Is it the licence issue?

Regards,

KK

[guoyun...@gmail.com]

Hi KK,

Mutect did not fit well two years ago when I developed seqmule. But Mutect will be supported in future versions of seqmule for sure. 

Thanks. 

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[Loke Kok Keong]

Hi Guo,

      Good to hear that, but I think now I should be able to manually run Mutect and apply with seqmule stats right? Please advise.

      Another point is do you aware of SomaticSeq? It support quite a few extra variant callers that seqmule can incorporate in future, thus can link both Seqmule and SomaticSeq into a single pipeline. That is why I come to ask for Mutect support in the first place.

Regards,

KK

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Loke Kok Keong
PhD Candidate of Computational Systems Biology
Centre for Bioinformatics Research (CBR)
Institute of Systems Biology (INBIOSIS)
Universiti Kebangsaan Malaysia (UKM)
43600 Bangi
Selangor
Malaysia
HP: 0102266792
kk86b...@gmail.com

[Yunfei Guo]

Hi KK,

Yes as long as the output complies with VCF 4.1 format supported by VCFtools and GATKLite.

Thanks for letting me know SomaticSeq. I will think about it. As long as it is easy to be installed and configured, it can be integrated.

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Best wishes,

Yunfei