jvarkit

SamToPsl

Convert SAM/BAM to PSL http://genome.ucsc.edu/FAQ/FAQformat.html#format2 or BED12

DEPRECATED

use bedtools/bamtobed

Usage

Usage: sam2psl [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
    -s, --single
      treat all reads as single end.
      Default: false
    --version
      print version and exit
    -B, bed12
      Export as BED 12.
      Default: false

Keywords

• sam
• bam
• psl

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 sam2psl

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

Creation Date

20140404

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/SamToPsl.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/SamToPslTest.java

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 sam2psl ? 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

Motivation

Convert SAM/BAM to PSL http://genome.ucsc.edu/FAQ/FAQformat.html#format2 or BED12 .

Properly-paired reads are extended to the mate’s position.

What ? bamtobed http://bedtools.readthedocs.org/en/latest/content/tools/bamtobed.html does the same job ?! too late.

Cited in:

• “R2C2: Improving nanopore read accuracy enables the sequencing of highly-multiplexed full-length single-cell cDNA” biorxiv https://doi.org/10.1101/338020
• Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Example

$ samtools view -b  http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200AlnRep1.bam "chr15:81575506-81616397" |\
   java -jar ~/src/jvarkit-git/dist/sam2psl.jar -s   > out.psl

$ tail out.psl
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:1105:11756:193850_2:N:0:/2_147	101	0	101	chr15	10349497481616327	81622456	3	1,5,95,	0,1,6,	81616327,81616393,81622362,
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:1301:4643:94800_2:N:0:/2_147	101	0	101	chr15	103494974	81616334	81622456	3	1,5,95,	0,1,6,	81616334,81616393,81622362,
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:1308:18580:185579_2:Y:0:/2_147	101	0	101	chr15	10349497481616327	81622456	3	1,5,95,	0,1,6,	81616327,81616393,81622362,
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:2205:10117:76559_2:N:0:/2_147	101	0	101	chr15	10349497481616321	81622456	3	1,5,95,	0,1,6,	81616321,81616393,81622362,
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:2206:7885:15613_2:N:0:/2_403	101	0	101	chr15	103494974	81613633	81622456	3	1,5,95,	0,1,6,	81613633,81616393,81622362,
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:2206:7885:15613_2:N:0:/2_147	101	0	101	chr15	103494974	81616308	81622456	3	1,5,95,	0,1,6,	81616308,81616393,81622362,
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:2303:12879:149117_1:Y:0:/1_83	101	0	101	chr15	10349497481616334	81622456	3	1,5,95,	0,1,6,	81616334,81616393,81622362,
6064	0	0	0	0	0	0	5964	+	HWI-ST0787:100:C02F9ACXX:3:1301:11600:100190_1:N:0:/1_99	100	0	100	chr15	10349497481616393	81622457	2	4,96,	0,4,	81616393,81622361,
6064	0	0	0	0	0	0	5964	+	HWI-ST0787:100:C02F9ACXX:3:2304:5980:187674_1:Y:0:/1_99	100	0	100	chr15	103494974	81616393	81622457	2	4,96,	0,4,	81616393,81622361,
6065	0	0	0	0	0	0	5964	-	HWI-ST0787:100:C02F9ACXX:3:1306:18607:99733_2:N:0:/2_147	101	0	101	chr15	10349497481616334	81622457	3	1,4,96,	0,1,5,	81616334,81616394,81622362,

used as a custom track in the UCSC genome browser.

See also

• bedtools/bamtobed : http://bedtools.readthedocs.org/en/latest/content/tools/bamtobed.html

Cited in

• “Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)
• Ashley Byrne, Megan A Supple, Roger Volden, Kristin L Laidre, Beth Shapiro, Christopher Vollmers” bioRxiv 527978; doi: https://doi.org/10.1101/527978
• Building A Better Transcriptome. Byrne, Ashley . 2019. Thesis. “https://escholarship.org/content/qt71z3w6dc/qt71z3w6dc.pdf”

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