SamToPsl

Last commit

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

DEPRECATED

use bedtools/bamtobed

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar sam2psl  [options] Files

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/gatk CreateSequenceDictionary or samtools dict
    -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

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

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/jvarkit.jar sam2psl -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.

img

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"