Split README-alt.md into two documentations
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Heng Li
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## Getting Started
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## For the Impatient
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```sh
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# Download the bwa-0.7.11 binary package
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# Download the bwa-0.7.11 binary package (download link may change)
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wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit-0.7.11_x64-linux.tar.bz2/download \
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| gzip -dc | tar xf -
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# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
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@ -11,22 +11,9 @@ bwa.kit/bwa index hs38d6.fa # create BWA index
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bwa.kit/run-bwamem -o out hs38d6.fa read1.fq read2.fq | sh # skip "|sh" to show command lines
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```
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This will generate the following files:
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* `out.aln.bam`: unsorted alignments with ALT-aware mapping quality. In this
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file, one read may be placed on multiple overlapping ALT contigs at the same
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time even if the read is mapped better to some contigs than others. This makes
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it possible to analyze each contig independent of others.
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* `out.hla.top`: best genotypes for HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 genes.
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* `out.hla.all`: other possible genotypes on the six HLA genes.
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* `out.log.*`: bwa-mem, samblaster and HLA typing log files.
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Note that `run-bwamem` only prints command lines but doesn't execute them. It
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is advised to have a look at the command lines before passing them to `sh` for
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actual execution.
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This generates `out.aln.bam` as the final alignment, `out.hla.top` for best HLA
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genotypes on each gene and `out.hla.all` for other possible HLA genotypes.
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Please check out [bwa/bwakit/README.md][kithelp] for details.
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## Background
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@ -57,7 +44,7 @@ postprocessing. The `bwa.kit/run-bwamem` script performs the two steps when ALT
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contigs are present. The following picture shows an example about how BWA-MEM
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infers mapping quality and reports alignment after step 2:
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#### Step 1: BWA-MEM mapping
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@ -189,3 +176,4 @@ can even get rid of ALT contigs for good.
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[hla2]: http://nar.oxfordjournals.org/content/41/14/e142.full.pdf+html
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[hla3]: http://www.biomedcentral.com/1471-2164/15/325
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[hla4]: http://genomemedicine.com/content/4/12/95
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[kithelp]: https://github.com/lh3/bwa/tree/master/bwakit
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@ -0,0 +1,50 @@
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Bwakit is a self-consistent installation-free package of scripts and precompiled
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binaries which provide an end-to-end solution to read mapping. In addition to
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the basic mapping functionality implemented in bwa, bwakit is able to generate
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proper human reference genome and to take advantage of ALT contigs, if present,
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to improve read mapping and to perform HLA typing for high-coverage human data.
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It can remap name- or coordinate-sorted BAM with read group and barcode
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information retained. Bwakit also *optionally* trims adapters (via
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[trimadap][ta]), marks duplicates (via [samblaster][sb]) and sorts the final
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alignment (via [samtools][smtl]).
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Bwakit has two entry scripts: `run-gen-ref` which downloads and generates human
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reference genomes, and `run-bwamem` which prints mapping command lines on the
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standard output that can be piped to `sh` to execute. The two scripts will call
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other programs or use data in `bwa.kit`. The following shows an example about
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how to use bwakit:
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```sh
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# Download the bwa-0.7.11 binary package (download link may change)
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wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.11_x64-linux.tar.bz2/download \
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| gzip -dc | tar xf -
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# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
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bwa.kit/run-gen-ref hs38d6 # download GRCh38 and write hs38d6.fa
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bwa.kit/bwa index hs38d6.fa # create BWA index
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# mapping
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bwa.kit/run-bwamem -o out hs38d6.fa read1.fq read2.fq | sh
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```
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The last mapping command line will generate the following files:
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* `out.aln.bam`: unsorted alignments with ALT-aware mapping quality. In this
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file, one read may be placed on multiple overlapping ALT contigs at the same
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time even if the read is mapped better to some contigs than others. This makes
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it possible to analyze each contig independent of others.
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* `out.hla.top`: best genotypes for HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 genes.
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* `out.hla.all`: other possible genotypes on the six HLA genes.
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* `out.log.*`: bwa-mem, samblaster and HLA typing log files.
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Bwakit can be [downloaded here][res]. It is only available to x86_64-linux. The
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scripts in the package are available in the [bwa/bwakit][kit] directory.
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Packaging is done manually for now.
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[res]: https://sourceforge.net/projects/bio-bwa/files/
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[sb]: https://github.com/GregoryFaust/samblaster
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[ta]: https://github.com/lh3/seqtk/blob/master/trimadap.c
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[smtl]: http://www.htslib.org
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[kit]: https://github.com/lh3/bwa/tree/master/bwakit
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