Biostar9608448

Convert long reads to short paired reads

Usage

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

Usage: java -jar dist/jvarkit.jar biostar9608448  [options] Files

Usage: biostar9608448 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --read-length, -L
      short read length
      Default: 150
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --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;,]'
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --version
      print version and exit

Keywords

• sam
• bam
• paired
• long
• illumina
• nanopore

See also in Biostars

• https://www.biostars.org/p/9608448

Creation Date

20250130

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar9608448.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 biostar9608448 ? 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 single end long read to paired end reads.

Note that short single read, paired reads, unmapped read, secondary & supplementary alignements are discarded

Example:

$ java -jar dist/jvarkit.jar  biostar9608448 src/test/resources/FAB23716.nanopore.bam -L 10 | samtools view | head
44767a9a-a0b9-4d7e-a324-d0d3ea113d8c_Basecall_Alignment_template    67  chr1    17123   38  6M2D4M  =   31047   13925   GTGCGCCGCT  -2.1.,(')-  MC:Z:10M
44767a9a-a0b9-4d7e-a324-d0d3ea113d8c_Basecall_Alignment_template    147 chr1    31047   38  10M =   17123   -13925  CACCTTGAAC  &#&$$$%$$%  MC:Z:6M2D4M
d324a4bc-aa2c-4ee8-be69-934cc58c0003_Basecall_Alignment_template    67  chr1    38469   1   10M =   43735   5267    ATGCTGCCTG  2-,.314443  MC:Z:10M
d324a4bc-aa2c-4ee8-be69-934cc58c0003_Basecall_Alignment_template    147 chr1    43735   1   10M =   38469   -5267   AGCAAACTTT  -',12()./.  MC:Z:10M
76862e2e-98eb-4ad3-a523-6a8709c0b56a_Basecall_Alignment_template    67  chr1    44403   0   10M =   44481   79  TCAACAACAA  &&&%&)'''&  MC:Z:10M
76862e2e-98eb-4ad3-a523-6a8709c0b56a_Basecall_Alignment_template    147 chr1    44481   0   10M =   44403   -79 GGTAGCCGAA  ''&$%(((%*  MC:Z:10M
3330d9a6-d2a9-423b-accc-92a6d1fe646e_Basecall_Alignment_template    67  chr1    52105   1   8M2D2M  =   53738   1634    ATTCCTACGA  %).,.%+$))  MC:Z:10M
3330d9a6-d2a9-423b-accc-92a6d1fe646e_Basecall_Alignment_template    147 chr1    53738   1   10M =   52105   -1634   ACTTAGGCAA  ,)((%%''((  MC:Z:8M2D2M
c6055e6a-9a1c-4126-84ec-64549fd4d264_Basecall_Alignment_template    67  chr1    63945   5   10M =   67887   3943    TCACCATGAT  *+'*-.111-  MC:Z:10M
c6055e6a-9a1c-4126-84ec-64549fd4d264_Basecall_Alignment_template    147 chr1    67887   5   10M =   63945   -3943   AGTATTATCA  +$+*+/((*&  MC:Z:10M