diff --git a/NEWS.md b/NEWS.md index 095b2de..cf2f468 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,21 +1,26 @@ -Release 0.7.11 (16 September, 2014) +Release 0.7.11 (XX September, 2014) ----------------------------------- A major change to BWA-MEM is the support of mapping to ALT contigs. To use this -feature, users need to manually create a file ".alt" with each line -giving the name of an ALT contig. In mapping, BWA-MEM considers all chromosomes -and contigs equally when it finds seeds, constructs chains, extends seeds and -derives the final alignments. It also uses all hits for the estimation of -mapping quality of ALT hits. However, BWA-MEM ignores ALT hits when it -estimates the mapping quality of hits to the primary assembly. As a result, -having ALT contigs almost has not effect on alignments to the primary assembly -(seeding may be affected in rare corner cases). At the same time, users may -get a primary alignment to ALT contigs (no 0x800 flag) if there are no good -hits to the primary assembly, or get a supplementary alignment to ALT contigs -if it is better than hits to the primary assembly. In the latter case, the -`pa:f` tag shows the ratio of the primary hit score to the best ALT hit score, -which is no greater than 1. Since this release, it is recommended to include -ALT contigs. +feature, users need to manually create a file ".alt" with each line +giving the name of an ALT contig. During alignment, BWA-MEM will be able to +classify potential hits to ALT and non-ALT hits. It reports alignments and +assigns mapping quality (mapQ) loosely following these rules: + + 1. The original mapQ of a non-ALT hit is computed across non-ALT hits only. + The reported mapQ of an ALT hit is always computed across all hits. + + 2. An ALT hit is only reported if its score is strictly better than all + overlapping non-ALT hits. A reported ALT hit is flagged with 0x800 + (supplementary) unless there are no non-ALT hits. + + 3. The mapQ of a non-ALT hit is reduced to zero if its score is less than 80% + (controlled by option `-g`) of the score of an overlapping ALT hit. In this + case, the original mapQ is moved to the `om` tag. + +This way, non-ALT alignments are only affected by ALT contigs if there are +significantly better ALT alignments. BWA-MEM is carefully engineered such that +ALT contigs do not interfere with the alignments to the primary assembly. Users may consider to use ALT contigs from GRCh38. I am also constructing a non-redundant and more complete set of sequences missing from GRCh38. @@ -32,12 +37,12 @@ Other notable changes to BWA-MEM: * Dropped PacBio read-to-read alignment for now. BWA-MEM is only good at finding the best hit, not all hits. Option `-x pbread` is still available, - but not shown on the command line. + but hidden on the command line. * Added new pre-setting for Oxford Nanopore 2D reads. For small genomes, though, LAST is still more sensitive. -(0.7.11: 16 September 2014, r845) +(0.7.11: XX September 2014, rXXX)