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Merge branch 'dev'

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Heng Li 2014-11-19 12:54:30 -05:00
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README-alt.md
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```sh ```sh
# Download the bwa-0.7.11 binary package (download link may change) # 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 - | gzip -dc | tar xf -
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index # Generate the GRCh38+ALT+decoy+HLA and create the BWA index
bwa.kit/run-gen-ref hs38d6 # download GRCh38 and write hs38d6.fa 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 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. 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 ## 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 [sb]: https://github.com/GregoryFaust/samblaster
[grc]: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ [grc]: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/
[novel]: https://gist.github.com/lh3/9935148b71f04ba1a8cc [novel]: https://gist.github.com/lh3/9935148b71f04ba1a8cc