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added another paper

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Heng Li 2014-10-23 15:15:20 -04:00
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@ -156,9 +156,9 @@ 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], [Bai and type HLA genes with another program, such as [Warren et al (2012)][hla4],
et al (2014)][hla3], [Dilthey et al (2014)][hla1] or one from [this [Liu et al (2013)][hla2], [Bai et al (2014)][hla3], [Dilthey et al (2014)][hla1]
list][hlatools]. or others 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
@ -198,3 +198,4 @@ can even get rid of ALT contigs for good.
[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 [hla3]: http://www.biomedcentral.com/1471-2164/15/325
[hla4]: http://genomemedicine.com/content/4/12/95