BWA
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Application data |
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| Created by | Heng Li and Richard Durbin |
|---|---|
| Biological application domain(s) | Mapping, Read alignment |
| Principal bioinformatics method(s) | FM-Index |
| Technology | Sanger, Illumina, 454, ABI SOLiD |
| Created at | Sanger Institute |
| Maintained? | Yes |
| Input format(s) | compressed/uncompressed fastq/fasta |
| Output format(s) | SAM |
| Software features | Gapped alignment, paired-end mapping |
| Programming language(s) | C |
| Licence | GPLv3, MIT |
| Operating system(s) | Unix |
Summary: Fast, accurate, memory-efficient aligner for short and long sequencing reads
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Contents
Notes
Ambiguous bases in reference sequences
According to the BWA paper, "Non-A/C/G/T bases on the reference genome are converted to random nucleotides."
BWA uses a fixed seed for the random number generator. This means that running bwa index twice on the same FASTA file will result in the same index.
(The seed is set to 11 in bntseq.c.)
XT:A tag
N stands for for BWA_TYPE_NO_MATCH (bwtaln.h). If the number of ambiguous bases in the reference (XN:i tag) is greater than 10, this tag is also set to N.
NM, CM tags
If "-c" was given on the command line, CM is written and NM otherwise (the tags are mutually exclusive).
XC:i tag
The XC:i tag is output when the clipped length of a read is less than the full read length.
XO, XG tags
Documentation says that XG is the number gap extensions. The source code seems to indicate that XG is the total no. of gaps (open+extend) (bwase.c):
printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
Regular index vs. color space index
A color space index (created with the -c option to bwa index) and a regular index cannot coexist in the same directory unless different prefixes are chosen (with the -p option).
Length of contig names
Contig names must not be longer than 1024 characters. If a name is longer, there is no error message, but it still does not work.
Unapplied Patches
- paired-end patch plus [1]
Links
- BWA Related [ edit link ]
- BWA Homepage [ edit link ]
References
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