Question: Is it Ok to use alignment BAM files from NextGene to produce variant calling with other tools or vice versa?
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gravatar for vassialk
4.4 years ago by
vassialk190
Belarus
vassialk190 wrote:

Is it Ok to use alignment files from NextGene to produce variant calling with other tools or vice versa: to call variants produced with bwa or bbmap with NexGene? Still could not find a GUI tool to do fast accurate wg to wg alignment, variant calling and reporting. Ugene is slow and Nextgene cuts wg as short reads. CLC and DNAStar are slow on i7 and i5 processors. Thx.

sequencing wgs • 976 views
ADD COMMENTlink modified 4.4 years ago by Istvan Albert ♦♦ 82k • written 4.4 years ago by vassialk190
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gravatar for Istvan Albert
4.4 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

Yes in theory. The whole point of the SAM standard is to support that.

In practice the reality is more complicated. Only the 11 columns of a SAM file are required by default, there could be a wealth of information in the additional optional tags. A variant caller may use those or not and depending the existence of those may work better or not so well.

All tools should produce reasonable results with inputs in a valid format. But again sometimes in practice that does not work out that well.

ADD COMMENTlink written 4.4 years ago by Istvan Albert ♦♦ 82k
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