updated ALT readme due to recent changes
This commit is contained in:
Heng Li
parent
76a15ea91b
commit
4260699a09
|
|
@ -3,7 +3,7 @@
|
|||
Since version 0.7.11, BWA-MEM supports read mapping against a reference genome
|
||||
with long alternative haplotypes present in separate ALT contigs. To use the
|
||||
ALT-aware mode, users need to provide pairwise ALT-to-reference alignment in the
|
||||
SAM format and rename the file to ""*idxbase*.alt". For GRCh38, this alignment
|
||||
SAM format and rename the file to "*idxbase*.alt". For GRCh38, this alignment
|
||||
is available from the [BWA resource bundle for GRCh38][res].
|
||||
|
||||
#### Option 1: Mapping to the official GRCh38 with ALT contigs
|
||||
|
|
@ -20,7 +20,6 @@ cp bwa-hs38-res/hs38d4.fa.alt hs38a.fa.alt
|
|||
Perform mapping:
|
||||
```sh
|
||||
bwa mem hs38a.fa read1.fq read2.fq \
|
||||
| samblaster \
|
||||
| bwa-hs38-res/k8-linux bwa-postalt.js hs38a.fa.alt \
|
||||
| samtools view -bS - > aln.unsrt.bam
|
||||
```
|
||||
|
|
@ -38,15 +37,14 @@ cp bwa-hs38-res/hs38d4.fa.alt .
|
|||
Perform mapping:
|
||||
```sh
|
||||
bwa mem hs38d4.fa read1.fq read2.fq \
|
||||
| samblaster \
|
||||
| bwa-hs38-res/k8-linux bwa-postalt.js -p postinfo hs38d4.fa.alt \
|
||||
| samtools view -bS - > aln.unsrt.bam
|
||||
```
|
||||
This command line generates `postinfo.ctw` which loosely evaluates the presence
|
||||
of an ALT contig with an empirical score at the last column.
|
||||
|
||||
**If you are not interested in the way BWA-MEM performs ALT mapping, you can
|
||||
skip the rest of this documentation.**
|
||||
***If you are not interested in the way BWA-MEM performs ALT mapping, you can
|
||||
skip the rest of this documentation.***
|
||||
|
||||
## Background
|
||||
|
||||
|
|
@ -80,20 +78,19 @@ the ALT-to-ref alignment, and labels a potential hit as *ALT* or *non-ALT*,
|
|||
depending on whether the hit lands on an ALT contig or not. BWA-MEM then reports
|
||||
alignments and assigns mapQ following these two rules:
|
||||
|
||||
* The original mapQ of a non-ALT hit is computed across non-ALT hits only.
|
||||
1. The original mapQ of a non-ALT hit is computed across non-ALT hits only.
|
||||
The reported mapQ of an ALT hit is computed across all hits.
|
||||
|
||||
* 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.
|
||||
2. If there are no non-ALT hits, the best ALT hit is outputted as the primary
|
||||
alignment. If there are both ALT and non-ALT hits, non-ALT hits will be
|
||||
primary. ALT hits are reported as supplementary alignments (flag 0x800) only
|
||||
if they are better than all overlapping non-ALT hits.
|
||||
|
||||
When option `-g FLOAT` is in use (which is the default), a third rule kicks in:
|
||||
In theory, non-ALT alignments from step 1 should be identical to alignments
|
||||
against a reference genome with ALT contigs. In practice, the two types of
|
||||
alignments may differ in rare cases due to seeding heuristics.
|
||||
|
||||
* The mapQ of a non-ALT hit is reduced to zero if its score is less than FLOAT
|
||||
times the score of an overlapping ALT hit. In this case, the original mapQ is
|
||||
moved to the `om` tag.
|
||||
|
||||
If we don't care about ALT hits, we may actually skip postprocessing (step 2).
|
||||
If we don't care about ALT hits, we may skip postprocessing (step 2).
|
||||
Nonetheless, postprocessing is recommended as it improves mapQ and gives more
|
||||
information about ALT hits.
|
||||
|
||||
|
|
@ -103,8 +100,9 @@ Postprocessing is done with a separate script `bwa-postalt.js`. It reads all
|
|||
potential hits reported in the XA tag, lifts ALT hits to the chromosomal
|
||||
positions using the ALT-to-ref alignment, groups them after lifting and then
|
||||
reassigns mapQ based on the best scoring hit in each group with all the hits in
|
||||
a group get the same mapQ. Knowing the ALT-to-ref alignment, this script can
|
||||
greatly improve mapQ of ALT hits and occasionally improve mapQ of non-ALT hits.
|
||||
a group get the same mapQ. Being aware of the ALT-to-ref alignment, this script
|
||||
can greatly improve mapQ of ALT hits and occasionally improve mapQ of non-ALT
|
||||
hits.
|
||||
|
||||
The script also measures the presence of each ALT contig. For a group of
|
||||
overlapping ALT contigs c_1, ..., c_m, the weight for c_k equals `\frac{\sum_j
|
||||
|
|
@ -134,6 +132,10 @@ In addition to decoy, we also put multiple alleles of HLA genes in
|
|||
version 3.18.0. Script `bwa-postalt.js` also helps to genotype HLA genes, though
|
||||
not to high resolution for now.
|
||||
|
||||
### Evaluating ALT Mapping
|
||||
|
||||
(To come later...)
|
||||
|
||||
## Problems and Future Development
|
||||
|
||||
There are some uncertainties about ALT mappings - we are not sure whether they
|
||||
|
|
@ -141,9 +143,10 @@ help biological discovery and don't know the best way to analyze them. Without
|
|||
clear demand from downstream analyses, it is very difficult to design the
|
||||
optimal mapping strategy. The current BWA-MEM method is just a start. If it
|
||||
turns out to be useful in research, we will probably rewrite bwa-postalt.js in C
|
||||
for performance; if not, we will try new designs. It is also possible that we
|
||||
may make breakthrough on the representation of multiple genomes, in which case,
|
||||
we can even get rid of ALT contigs once for all.
|
||||
for performance; if not, we may make changes. It is also possible that we might
|
||||
make breakthrough on the representation of multiple genomes, in which case, we
|
||||
can even get rid of ALT contigs for good.
|
||||
|
||||
|
||||
|
||||
[res]: https://sourceforge.net/projects/bio-bwa/files/
|
||||
|
|
|
|||
Loading…
Reference in New Issue