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Updated READMEs a little

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Heng Li 2014-12-01 09:50:47 -05:00
parent 9d8c906e4c
commit d6e8e5929b
4 changed files with 9 additions and 5 deletions
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README-alt.md
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@ -1,7 +1,7 @@
## For the Impatient
```sh
# Download the bwa-0.7.11 binary package (download link may change)
# Download bwakit (or from <http://sourceforge.net/projects/bio-bwa/files/bwakit/> 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

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README.md
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@ -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)
####<a name="type"></a>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.
####<a name="altctg"></a>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

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bwakit/README.md
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@ -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 <http://sourceforge.net/projects/bio-bwa/files/bwakit/> 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

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bwa-postalt.js → bwakit/bwa-postalt.js
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