From 3a1da27c1cc1fae4517da93a767b77a00ef270ff Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 23 Oct 2014 15:08:18 -0400 Subject: [PATCH] added Bai et al. Seems good, too. --- README-alt.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/README-alt.md b/README-alt.md index 35d9f4c..772766e 100644 --- a/README-alt.md +++ b/README-alt.md @@ -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