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added Bai et al. Seems good, too.

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Heng Li 2014-10-23 15:08:18 -04:00
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README-alt.md
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@ -156,14 +156,16 @@ have ignored these important genes.
We recommend to include the genomic regions of classical HLA genes in the BWA
index. This way we will be able to get a more complete collection of reads
mapped to HLA. We can then isolate these reads with little computational cost
and type HLA genes with another program, such as [Liu et al (2013)][hla2],
[Dilthey et al (2014)][hla1] or one from [this list][hlatools].
and type HLA genes with another program, such as [Liu et al (2013)][hla2], [Bai
et al (2014)][hla3], [Dilthey et al (2014)][hla1] or one from [this
list][hlatools].
If the postprocessing script `bwa-postalt.js` is invoked with `-p prefix`, it
will also write the top three alleles to file `prefix.hla`. However, as most HLA
alleles from IMGT/HLA don't have intronic sequences and thus are not included in
the reference genome, we are unable to type HLA genes to high resolution with
the BWA-MEM mapping alone. A dedicated tool is recommended for accurate typing.
the BWA index from option 2, we are unable to type HLA genes to high resolution
with the BWA-MEM mapping alone. A dedicated tool is recommended for accurate
typing.
### Evaluating ALT Mapping
@ -195,3 +197,4 @@ can even get rid of ALT contigs for good.
[hlalink]: http://www.hladiseaseassociations.com
[hlatools]: https://www.biostars.org/p/93245/
[hla2]: http://nar.oxfordjournals.org/content/41/14/e142.full.pdf+html
[hla3]: http://www.biomedcentral.com/1471-2164/15/325