From 393735d7f18b2895df966c31bf06debee98fef8d Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 2 Dec 2014 10:30:35 -0500 Subject: [PATCH] more FAQs on ALT mapping --- README.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index eb81609f..9ac49bbe 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,7 @@ do not have plan to submit it to a peer-reviewed journal in the near future. 4. [Why can one read in a pair has high mapping quality but the other has zero?](#pe0) 5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref) 6. [Does BWA work with ALT contigs in the GRCh38 release?](#altctg) +7. [Can I just run BWA-MEM against GRCh38+ALT without post-processing?](#postalt) ####1. What types of data does BWA work with? @@ -136,7 +137,21 @@ as well. BWA-MEM does not have this problem. ####6. Does BWA work with ALT contigs in the GRCh38 release? -Yes, since 0.7.11. Please see [README-alt.md][18] for details. +Yes, since 0.7.11, BWA-MEM officially supports mapping to GRCh38+ALT. +BWA-backtrack and BWA-SW don't properly support ALT mapping as of now. Please +see [README-alt.md][18] for details. Briefly, it is recommended to use +[bwakit][17], the binary release of BWA, for generating the reference genome +and for mapping. + +####7. Can I just run BWA-MEM against GRCh38+ALT without post-processing? + +If you are not interested in hits to ALT contigs, it is okay to run BWA-MEM +without post-processing. The alignments produced this way are very close to +alignments against GRCh38 without ALT contigs. Nonetheless, applying +post-processing helps to reduce false mappings caused by reads from the +diverged part of ALT contigs and also enables HLA typing. It is recommended to +run the post-processing script. + [1]: http://en.wikipedia.org/wiki/GNU_General_Public_License