jvarkit

Sam2Tsv

Last commit

Prints the SAM alignments as a TAB delimited file.

Usage

Usage: sam2tsv [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --regions
      Limit analysis to this interval. A source of intervals. The following 
      suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz, 
      gtf.gz.Otherwise it could be an empty string (no interval) or a list of 
      plain interval separated by '[ \t\n;,]'
    -N, --skip-N
      Skip 'N' operator
      Default: false
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --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 sam2tsv

The java jar file will be installed in the dist directory.

Creation Date

20170712

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2TsvTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite sam2tsv ? 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/sam2tsv.jar -R src/test/resources/toy.fa src/test/resources/toy.bam 


#Read-Name  Flag  MAPQ  CHROM  READ-POS0  READ-BASE  READ-QUAL  REF-POS1  REF-BASE  CIGAR-OP
r001        163   30    ref    0          T          .          7         T         M
r001        163   30    ref    1          T          .          8         T         M
r001        163   30    ref    2          A          .          9         A         M
r001        163   30    ref    3          G          .          10        G         M
r001        163   30    ref    4          A          .          11        A         M
r001        163   30    ref    5          T          .          12        T         M
r001        163   30    ref    6          A          .          13        A         M
r001        163   30    ref    7          A          .          14        A         M
r001        163   30    ref    8          A          .          .         .         I
r001        163   30    ref    9          G          .          .         .         I
r001        163   30    ref    10         A          .          .         .         I
r001        163   30    ref    11         G          .          .         .         I
r001        163   30    ref    12         G          .          15        G         M
r001        163   30    ref    13         A          .          16        A         M
r001        163   30    ref    14         T          .          17        T         M
r001        163   30    ref    15         A          .          18        A         M
r001        163   30    ref    .          .          .          19        G         D
r001        163   30    ref    16         C          .          20        C         M
r001        163   30    ref    17         T          .          21        T         M
r001        163   30    ref    18         G          .          22        G         M
r002        0     30    ref    0          A          .          8         T         S
r002        0     30    ref    1          A          .          .         .         I
r002        0     30    ref    2          A          .          .         .         I
r002        0     30    ref    3          A          .          9         A         M
r002        0     30    ref    4          G          .          10        G         M
r002        0     30    ref    5          A          .          11        A         M
r002        0     30    ref    6          T          .          12        T         M
r002        0     30    ref    7          A          .          13        A         M
r002        0     30    ref    8          A          .          14        A         M
r002        0     30    ref    .          .          .          .         .         P
r002        0     30    ref    9          G          .          .         .         I
r002        0     30    ref    .          .          .          .         .         P
r002        0     30    ref    10         G          .          .         .         I
r002        0     30    ref    11         G          .          15        G         M
r002        0     30    ref    12         A          .          16        A         M
(...)

Example 2

sam2tsv can read data from a linux pipe.

samtools view -h input.bam | java -jar dist/sam2tsv.jar

Citations

Sam2tsv was cited in :