jvarkit
BlastNToSnp
print indel/mismatch in a blastn stream
Usage
Usage: java -jar dist/blastn2snp.jar [options] Files
Usage: blastn2snp [options] Files
Options:
-n, --gapsize
min gap
Default: 3
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
Keywords
- blast
- snp
See also in Biostars
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew blastn2snp
The java jar file will be installed in the dist directory.
Creation Date
20131126
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite blastn2snp ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Example
$ java -jar dist/blastn2snp.jar < blast.xml | column -t
#query hit hit-index hsp-index query-POS hit-POS STRAND REF(hit) ALT(query) blast.align_length blast.hit.var blast.query.var blast.mid.var
No definition line Homo sapiens chromosome 6, alternate assembly CHM1_1.1 1 9 21 74567818 - T A 18 A T .
No definition line Homo sapiens chromosome 6, alternate assembly HuRef 2 9 21 71600901 - T A 18 A T .
No definition line Homo sapiens chromosome 6, GRCh37.p13 Primary Assembly 3 9 21 74401398 - T A 18 A T .
No definition line Homo sapiens chromosome 5, alternate assembly CHM1_1.1 4 1 7 107821121 - A G 28 T C .
No definition line Homo sapiens chromosome 5, alternate assembly CHM1_1.1 4 9 16 14262358 + G C 18 G C .
No definition line Homo sapiens chromosome 5, alternate assembly CHM1_1.1 4 13 8 132662461 - T C 18 A G .
No definition line Homo sapiens chromosome 5, alternate assembly CHM1_1.1 4 20 14 170329095 - G C 18 C G .
No definition line Homo sapiens chromosome 5, alternate assembly HuRef 5 1 7 103561224 - A G 28 T C .
No definition line Homo sapiens chromosome 5, alternate assembly HuRef 5 9 16 14234054 + G C 18 G C .
No definition line Homo sapiens chromosome 5, alternate assembly HuRef 5 13 8 128416747 - T C 18 A G .
No definition line Homo sapiens chromosome 5, alternate assembly HuRef 5 19 14 165993804 - G C 18 C G .
No definition line Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly 6 1 7 108388040 - A G 28 T C .
No definition line Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly 6 9 16 14262514 + G C 18 G C .
No definition line Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly 6 13 8 133231874 - T C 18 A G .
No definition line Homo sapiens chromosome 5, GRCh37.p13 Primary Assembly 6 19 14 170896537 - G C 18 C G .
No definition line Homo sapiens chromosome 19, alternate assembly CHM1_1.1 8 13 18 54878835 - A C 18 T G .
No definition line Homo sapiens chromosome 19, alternate assembly CHM1_1.1 8 14 18 54999463 + T G 18 T G .
No definition line Homo sapiens chromosome 19, alternate assembly CHM1_1.1 8 15 21 55131801 - G A 18 C T .
No definition line Homo sapiens chromosome 19, alternate assembly HuRef 9 14 18 51207279 - A C 18 T G .
No definition line Homo sapiens chromosome 19, alternate assembly HuRef 9 15 18 51329261 + T G 18 T G .
No definition line Homo sapiens chromosome 19, alternate assembly HuRef 9 16 21 51461318 - G A 18 C T .
Cited in:
- Guo, Y., Betzen, B., Salcedo, A. et al. Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races. Nat Commun 13, 6287 (2022). https://doi.org/10.1038/s41467-022-34050-w