From 3633436a3d9505a25cf60b92d184d24ce60535f5 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 19 Nov 2014 12:54:15 -0500 Subject: [PATCH] added download link explicitly --- README-alt.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README-alt.md b/README-alt.md index 3460cdd..2d8fb40 100644 --- a/README-alt.md +++ b/README-alt.md @@ -2,7 +2,7 @@ ```sh # Download the bwa-0.7.11 binary package (download link may change) -wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit-0.7.11_x64-linux.tar.bz2/download \ +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 bwa.kit/run-gen-ref hs38d6 # download GRCh38 and write hs38d6.fa @@ -13,7 +13,8 @@ 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. +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]. ## Background @@ -161,7 +162,7 @@ can even get rid of ALT contigs for good. -[res]: https://sourceforge.net/projects/bio-bwa/files/ +[res]: https://sourceforge.net/projects/bio-bwa/files/bwakit [sb]: https://github.com/GregoryFaust/samblaster [grc]: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ [novel]: https://gist.github.com/lh3/9935148b71f04ba1a8cc