Question: BWA.KIT where can i find it? Very confused
0
gravatar for Duarte Molha
12 weeks ago by
Duarte Molha200
Oxford, UK
Duarte Molha200 wrote:

Hi everyone

I am thinking if testing the bwa.post processing for alt contigs provided by bwa.kit... but I am very confused

BWA kit releases can be downloaded from here:

https://sourceforge.net/projects/bio-bwa/files/bwakit

and it seems it is hosted now on github here

https://github.com/lh3/bwa/tree/master/bwakit

but if you go to the github page , they say the contents of the package are : these:

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
|   |-- hs38DH-extra.fa        Decoy and HLA gene sequences. Used by run-gen-ref.
|   `-- hs38DH.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

I have downloaded the files and this content is no where to be found. All it contains is the source files to make bwa and a subfolder with the bwa.kit scripts for alt mapping, index building and post processing

What am I missing?

bwakit bwa alt_mapping • 204 views
ADD COMMENTlink modified 12 weeks ago by finswimmer10k • written 12 weeks ago by Duarte Molha200
1
gravatar for finswimmer
12 weeks ago by
finswimmer10k
Germany
finswimmer10k wrote:

Hello Duarte Molha ,

where did you download? On github there are only the custom scripts by Heng Li hosted and not the additional binarys. The whole package is ready for download and contains all files you've listed above (and are mentioned on github).

fin swimmer

ADD COMMENTlink written 12 weeks ago by finswimmer10k

unfortunately this is not the case ,, take a look at the folder called doc and the resource-human-HLA. and the other resource folder

none of those folders are on the downloads ... i know I checked

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by Duarte Molha200

I've downloaded bwakit-0.7.15_x64-linux.tar.bz2 from this source. After extracting the content of the bwa.kit folder looks like this:

$ tree .
.
├── README.md
├── bwa
├── bwa-postalt.js
├── doc
│   ├── NEWS.md
│   ├── README-alt.md
│   ├── README.md
│   └── bwa.1
├── fermi2
├── fermi2.pl
├── htsbox
├── k8
├── resource-GRCh38
│   ├── hs38DH-extra.fa
│   └── hs38DH.fa.alt
├── resource-human-HLA
│   ├── HLA-ALT-exons.bed
│   ├── HLA-ALT-idx
│   │   ├── alt_APD.fa.amb
│   │   ├── alt_APD.fa.ann
│   │   ├── alt_APD.fa.bwt
│   │   ├── alt_APD.fa.pac
│   │   ├── alt_APD.fa.sa
│   │   ├── alt_COX.fa.amb
│   │   ├── alt_COX.fa.ann
│   │   ├── alt_COX.fa.bwt
│   │   ├── alt_COX.fa.pac
│   │   ├── alt_COX.fa.sa
│   │   ├── alt_DBB.fa.amb
│   │   ├── alt_DBB.fa.ann
│   │   ├── alt_DBB.fa.bwt
│   │   ├── alt_DBB.fa.pac
│   │   ├── alt_DBB.fa.sa
│   │   ├── alt_MANN.fa.amb
│   │   ├── alt_MANN.fa.ann
│   │   ├── alt_MANN.fa.bwt
│   │   ├── alt_MANN.fa.pac
│   │   ├── alt_MANN.fa.sa
│   │   ├── alt_MCF.fa.amb
│   │   ├── alt_MCF.fa.ann
│   │   ├── alt_MCF.fa.bwt
│   │   ├── alt_MCF.fa.pac
│   │   ├── alt_MCF.fa.sa
│   │   ├── alt_QBL.fa.amb
│   │   ├── alt_QBL.fa.ann
│   │   ├── alt_QBL.fa.bwt
│   │   ├── alt_QBL.fa.pac
│   │   ├── alt_QBL.fa.sa
│   │   ├── alt_SSTO.fa.amb
│   │   ├── alt_SSTO.fa.ann
│   │   ├── alt_SSTO.fa.bwt
│   │   ├── alt_SSTO.fa.pac
│   │   ├── alt_SSTO.fa.sa
│   │   ├── pri_PGF.fa.amb
│   │   ├── pri_PGF.fa.ann
│   │   ├── pri_PGF.fa.bwt
│   │   ├── pri_PGF.fa.pac
│   │   └── pri_PGF.fa.sa
│   ├── HLA-ALT-type.txt
│   └── HLA-CDS.fa
├── ropebwt2
├── run-HLA
├── run-bwamem
├── run-gen-ref
├── samblaster
├── samtools
├── seqtk
├── trimadap
├── typeHLA-selctg.js
├── typeHLA.js
└── typeHLA.sh

Looks quite similar like the list on github.

ADD REPLYlink written 12 weeks ago by finswimmer10k

Ok ... I think I got what is wrong. I downloaded what I thought was the latest version from that link (0.7.17 file)

But the bwakit is the file below at version 0.7.15

Many thanks

Feeling a bit of an idiot :)

ADD REPLYlink written 12 weeks ago by Duarte Molha200
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