jvarkit

ExtendReferenceWithReads

Extending ends of sequences with the help of reads

Usage

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

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

Usage: extendrefwithreads [options] Files
  Options:
    -f, --callingfraction
      (0.0<float<=1.0) new base must have fraction greater than this number
      Default: 0.8
    -filter, --filter
      A filter expression. Reads matching the expression will be filtered-out. 
      Empty String means 'filter out nothing/Accept all'. See https://github.com/lindenb/jvarkit/blob/master/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj 
      for a complete syntax. 'default' is 'mapqlt(1) || Duplicate() || 
      FailsVendorQuality() || NotPrimaryAlignment() || 
      SupplementaryAlignment()' 
      Default: mapqlt(1) || Duplicate() || FailsVendorQuality() || NotPrimaryAlignment() || SupplementaryAlignment()
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -N, --mincontig
      onsider only gaps in reference with size&gt;=N
      Default: 100
    -d, --mindepth
      min depth
      Default: 1
    -o, --out
      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
    --version
      print version and exit

Keywords

• read
• fastq
• reference
• sam
• bam

See also in Biostars

• https://www.biostars.org/p/148089

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/extendref/ExtendReferenceWithReads.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 extendrefwithreads ? 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/extendrefwithreads.jar \
 -R human_g1k_v37.fasta -f 0.3 \
 f1.bam f2.bam f3.bam 2> /dev/null |\
cat -n | grep -E '(>|[atgc])' 

 1	>1
167	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNncgattaccctaacgctcac
168	cctaaccctcnccctntnccnncnncccnncttcttccgaTAACCCTAACCCTAACCCTA
3791	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNatt
3792	tatgcNctttntgctgtGATTCATGGCTGAAATCGTGTTTGACCAGCTATGTGTGTCTCT
8691	NNNNNNNNNNNNNNNNNNNNNNNNctagGATCCTTGAAGCGCCCCCAAGGGCATCTTCTC
64089	TGGTGAGGGAAATTAGAACCACGACAATTTGGGAACTTAGCTTCTGCCctgctccNNNNN
66589	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNgagtAGCTGAGACTAC

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