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Merge branch 'dev'

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Heng Li 2014-11-19 12:47:20 -05:00
parent 8422950472 6609bafa17
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43
bwakit/README.md
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@ -1,3 +1,5 @@
## Introduction
Bwakit is a self-consistent installation-free package of scripts and precompiled
binaries, providing an end-to-end solution to read mapping. In addition to the
basic mapping functionality implemented in bwa, bwakit is able to generate
@ -42,6 +44,47 @@ Bwakit can be [downloaded here][res]. It is only available to x86_64-linux. The
scripts in the package are available in the [bwa/bwakit][kit] directory.
Packaging is done manually for now.
## Contents
```
bwa.kit
|-- README.md This README file.
|-- run-bwamem *Entry script* for the entire mapping pipeline.
|-- bwa *BWA binary*
|-- k8 Interpretor 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
|-- samtools SAMtools for sorting and SAM=>BAM conversion. v1.1
|-- seqtk For FASTQ manipulation.
|-- trimadap Trim Illumina PE sequencing adapters.
|
|-- run-gen-ref *Entry script* for generating human reference genomes.
|-- resource-GRCh38 Resources for generating GRCh38
| |-- hs38d6-decoy.nt.anno Top decoy-to-nt hits. Not used by any scripts.
| |-- hs38d6-decoy.rm.out RepeatMasker report. Not used.
| |-- hs38d6-extra.fa Decoy and HLA gene sequences. Used by run-gen-ref.
| `-- hs38d6.fa.alt ALT-to-GRCh38 alignment. Used by run-gen-ref.
|
|-- run-HLA HLA typing for sequences extracted by bwa-postalt.js.
|-- typeHLA.sh Type one HLA-gene. Called by run-HLA.
|-- typeHLA.js HLA typing from exon-to-contig alignment. Used by typeHLA.sh.
|-- typeHLA-selctg.js Select contigs overlapping HLA exons. Used by typeHLA.sh.
|-- fermi2.pl Fermi2 wrapper. Used by typeHLA.sh for de novo assembly.
|-- fermi2 Fermi2 binary. Used by fermi2.pl.
|-- ropebwt2 RopeBWT2 binary. Used by fermi2.pl.
|-- resource-human-HLA Resources for HLA typing
| |-- HLA-ALT-exons.bed Exonic regions of HLA ALT contigs. Used by typeHLA.sh.
| |-- HLA-CDS.fa CDS of HLA-{A,B,C,DQA1,DQB1,DRB1} genes from IMGT/HLA-3.18.0.
| |-- HLA-ALT-type.txt HLA types for each HLA ALT contig. Not used.
| `-- HLA-ALT-idx BWA indices of each HLA ALT contig. Used by typeHLA.sh
| `-- (...)
|
`-- doc BWA documentations
|-- bwa.1 Manpage
|-- NEWS.md Release Notes
|-- README.md GitHub README page
`-- README-alt.md Documentation for ALT mapping
```
[res]: https://sourceforge.net/projects/bio-bwa/files/bwakit
[sb]: https://github.com/GregoryFaust/samblaster

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bwakit/run-bwamem
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@ -55,6 +55,7 @@ my $idx = $ARGV[0];
my $exepath = $0 =~/^\S+\/[^\/\s]+/? $0 : &which($0);
my $root = $0 =~/^(\S+)\/[^\/\s]+/? $1 : undef;
$root = $exepath =~/^(\S+)\/[^\/\s]+/? $1 : undef if !defined($root);
die "ERROR: failed to locate the 'bwa.kit' directory\n" if !defined($root);
die("ERROR: failed to locate the BWA index. Please run '$root/bwa index -p $idx ref.fa'.\n")