diff --git a/README-alt.md b/README-alt.md
index 2d8fb40..088be47 100644
--- a/README-alt.md
+++ b/README-alt.md
@@ -1,7 +1,7 @@
## For the Impatient
```sh
-# Download the bwa-0.7.11 binary package (download link may change)
+# Download bwakit (or from manually)
wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.11_x64-linux.tar.bz2/download \
| gzip -dc | tar xf -
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
@@ -13,8 +13,7 @@ bwa.kit/run-bwamem -o out hs38d6.fa read1.fq read2.fq | sh # skip "|sh" to show
This generates `out.aln.bam` as the final alignment, `out.hla.top` for best HLA
genotypes on each gene and `out.hla.all` for other possible HLA genotypes.
-Please check out [bwa/bwakit/README.md][kithelp] for details. If the download
-link above does not work, please acquire the binary package [here][res].
+Please check out [bwa/bwakit/README.md][kithelp] for details.
## Background
diff --git a/README.md b/README.md
index 63391c1..eb81609 100644
--- a/README.md
+++ b/README.md
@@ -70,6 +70,7 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb)
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)
####1. What types of data does BWA work with?
@@ -133,6 +134,9 @@ case, BWA-backtrack will flag the read as unmapped (0x4), but you will see
position, CIGAR and all the tags. A similar issue may occur to BWA-SW alignment
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.
[1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
@@ -152,3 +156,4 @@ as well. BWA-MEM does not have this problem.
[15]: https://github.com/lh3/bwa/tree/mem
[16]: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/
[17]: http://sourceforge.net/projects/bio-bwa/files/bwakit/
+[18]: https://github.com/lh3/bwa/blob/master/README-alt.md
diff --git a/bwakit/README.md b/bwakit/README.md
index f16e74d..d56a9e4 100644
--- a/bwakit/README.md
+++ b/bwakit/README.md
@@ -17,7 +17,7 @@ other programs or use data in `bwa.kit`. The following shows an example about
how to use bwakit:
```sh
-# Download the bwa-0.7.11 binary package (download link may change)
+# Download bwakit (or from manually)
wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.11_x64-linux.tar.bz2/download \
| gzip -dc | tar xf -
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
@@ -50,7 +50,7 @@ bwa.kit
|-- README.md This README file.
|-- run-bwamem *Entry script* for the entire mapping pipeline.
|-- bwa *BWA binary*
-|-- k8 Interpretor for *.js scripts.
+|-- k8 Interpreter for *.js scripts.
|-- bwa-postalt.js Post-process alignments to ALT contigs/decoys/HLA genes.
|-- htsbox Used by run-bwamem for shuffling BAMs and BAM=>FASTQ.
|-- samblaster MarkDuplicates for reads from the same library. v0.1.20
diff --git a/bwa-postalt.js b/bwakit/bwa-postalt.js
similarity index 100%
rename from bwa-postalt.js
rename to bwakit/bwa-postalt.js