From 7c362bef69eba18d8064d9ae9f9c7ddded45cc00 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 23 Oct 2014 15:15:20 -0400 Subject: [PATCH] added another paper --- README-alt.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README-alt.md b/README-alt.md index 772766e..1ee2e9f 100644 --- a/README-alt.md +++ b/README-alt.md @@ -156,9 +156,9 @@ 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], [Bai -et al (2014)][hla3], [Dilthey et al (2014)][hla1] or one from [this -list][hlatools]. +and type HLA genes with another program, such as [Warren et al (2012)][hla4], +[Liu et al (2013)][hla2], [Bai et al (2014)][hla3], [Dilthey et al (2014)][hla1] +or others 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 @@ -198,3 +198,4 @@ can even get rid of ALT contigs for good. [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 +[hla4]: http://genomemedicine.com/content/4/12/95