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The following list gives the recommended settings:. Generally, BWA-MEM is more tolerant with errors given longer query sequences as the chance of missing all seeds is small. If there is a translocation, a gene fusion or a long deletion, a read bridging the break point may have two hits, occupying two lines in the SAM output. With the default setting of BWA-MEM, one and only one line is primary and is soft clipped; other lines are tagged with 0x SAM flag supplementary alignment and are hard clipped.
However, individual chromosome should not be longer than 2GB. This is correct. Mapping quality is assigned for individual read, not for a read pair. It is possible that one read can be mapped unambiguously, but its mate falls in a tandem repeat and thus its accurate position cannot be determined. Internally BWA concatenates all reference sequences into one long sequence.
A read may be mapped to the junction of two adjacent reference sequences. Yes, since 0. Briefly, it is recommended to use bwakit , the binary release of BWA, for generating the reference genome and for mapping.
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