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.
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.