Prints the SAM alignments as a TAB delimited file.
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, -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
-N, --skip-N
Skip 'N' operator
Default: false
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew sam2tsv
The java jar file will be installed in the dist
directory.
20170712
The project is licensed under the MIT license.
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
$ 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
(...)
sam2tsv can read data from a linux pipe.
samtools view -h input.bam | java -jar dist/sam2tsv.jar
Sam2tsv was cited in :