diff --git a/README-alt.md b/README-alt.md index 2d8fb40..088be47 100644 --- a/README-alt.md +++ b/README-alt.md @@ -1,7 +1,7 @@ ## For the Impatient ```sh -# Download the bwa-0.7.11 binary package (download link may change) +# Download bwakit (or from 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 diff --git a/README.md b/README.md index 63391c1..eb81609 100644 --- a/README.md +++ b/README.md @@ -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) ####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. +####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 diff --git a/bwakit/README.md b/bwakit/README.md index f16e74d..d56a9e4 100644 --- a/bwakit/README.md +++ b/bwakit/README.md @@ -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 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 diff --git a/bwa-postalt.js b/bwakit/bwa-postalt.js similarity index 100% rename from bwa-postalt.js rename to bwakit/bwa-postalt.js