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help on how to use bwa-helper.js

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Heng Li 2014-05-06 17:11:17 -04:00
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README.md
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@ -57,7 +57,39 @@ in forums such as [BioStar][8] and [SEQanswers][9].
Please note that the last reference is a preprint hosted at [arXiv.org][13]. I
do not have plan to submit it to a peer-reviewed journal in the near future.
###Frequently asked questions (FAQs)
####How to map sequences to GRCh38 with ALT contigs?
BWA-backtrack and BWA-MEM partially support mapping to a reference containing
ALT contigs that represent alternative alleles highly divergent from the
reference genome.
# download the K8 executable required by bwa-helper.js
wget http://sourceforge.net/projects/lh3/files/k8/k8-0.2.1.tar.bz2/download
tar -jxf k8-0.2.1.tar.bz2
# download the ALT-to-GRCh38 alignment in the SAM format
wget http://sourceforge.net/projects/bio-bwa/files/hs38.alt.sam.gz/download
# download the GRCh38 sequences with ALT contigs
wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz
# index and mapping
bwa index -p hs38a GCA_000001405.15_GRCh38_full_analysis_set.fna.gz
bwa mem -h50 hs38a reads.fq | ./k8-linux bwa-helper.js genalt hs38.alt.sam.gz > out.sam
Here, option `-h50` asks bwa-mem to output multiple hits in the XA tag if the
read has 50 or fewer hits. For each SAM line containing the XA tag,
`bwa-helper.js genalt` decodes the alignments in the XA tag, groups hits lifted
to the same chromosomal region, adjusts mapping quality and outputs all the
hits overlapping the reported hit. A read may be mapped to both the primary
assembly and one or more ALT contigs all with high mapping quality.
Note that this procedure assumes reads are single-end and may miss hits to
highly repetitive regions as these hits will not be reported with option
`-h50`. `bwa-helper.js` is a prototype implementation not recommended for
production uses.
[1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
[2]: https://github.com/lh3/bwa
@ -74,3 +106,4 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
[13]: http://arxiv.org/
[14]: http://zlib.net/
[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/