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updated release notes

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Heng Li 2014-09-18 11:51:52 -04:00
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NEWS.md
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@ -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 "<index>.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 "<indexbase>.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)