jvarkit

BlastNToSnp

Last commit

print indel/mismatch in a blastn stream

Usage

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

See also in Biostars

Compilation

Requirements / Dependencies

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.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnpTest.java

Contribute

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                .