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?
•
written
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Duarte Molha
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
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
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.
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 :)
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