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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 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 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 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], and type HLA genes with another program, such as [Liu et al (2013)][hla2], [Bai
[Dilthey et al (2014)][hla1] or one from [this list][hlatools]. 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 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 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 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 index from option 2, we are unable to type HLA genes to high resolution
the BWA-MEM mapping alone. A dedicated tool is recommended for accurate typing. with the BWA-MEM mapping alone. A dedicated tool is recommended for accurate
typing.
### Evaluating ALT Mapping ### Evaluating ALT Mapping
@ -195,3 +197,4 @@ can even get rid of ALT contigs for good.
[hlalink]: http://www.hladiseaseassociations.com [hlalink]: http://www.hladiseaseassociations.com
[hlatools]: https://www.biostars.org/p/93245/ [hlatools]: https://www.biostars.org/p/93245/
[hla2]: http://nar.oxfordjournals.org/content/41/14/e142.full.pdf+html [hla2]: http://nar.oxfordjournals.org/content/41/14/e142.full.pdf+html
[hla3]: http://www.biomedcentral.com/1471-2164/15/325