jvarkit

SamExtractClip

Extract Soft Clipped Sequences from a SAM. Ouput is a FASTQ

Usage

Usage: java -jar dist/samextractclip.jar  [options] Files
Usage: samextractclip [options] Files
  Options:
    -c, --clipped
      Print the original Read where the clipped regions have been removed.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -m, --minsize
      Min size of clipped read
      Default: 5
    -p, --original
      Print Original whole Read that contained a clipped region.
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -readFilter, --readFilter
      [20181208]A JEXL Expression that will be used to filter out some 
      sam-records (see 
      https://software.broadinstitute.org/gatk/documentation/article.php?id=1255). 
      An expression should return a boolean value (true=exclude, false=keep 
      the read). An empty expression keeps everything. The variable 'record' 
      is the current observed read, an instance of SAMRecord (https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html).
      Default: record.getMappingQuality()<1 || record.getDuplicateReadFlag() || record.getReadFailsVendorQualityCheckFlag() || record.isSecondaryOrSupplementary()
    -R, --reference
      For reading/writing CRAM files. Indexed fasta Reference file. This file 
      must be indexed with samtools faidx and with picard 
      CreateSequenceDictionary 
    --version
      print version and exit

Keywords

• sam
• bam
• fastq
• clip

See also in Biostars

• https://www.biostars.org/p/125874

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 samextractclip

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

Creation Date

20140228

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/SamExtractClip.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/SamExtractClipTest.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 samextractclip ? 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

$ curl -L -s "https://raw.githubusercontent.com/samtools/samtools/develop/test/dat/mpileup.1.sam" |\
	java -jar dist/samextractclip.jar 2> /dev/null 

@ERR013140.3521432/1:0:17:1:99
AGAGGTCCCCAACTTCTTTGCA
+
@AEDGBHIIIIIFJGIKHGHIJ
@ERR156632.12704932/2:0:17:1:163
TGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCA
+
BFAFGFEIGFEFHHEIDKJGHHHJIIE=@KKGGKJG
@ERR156632.9601178/1:0:17:1:99
CTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCA
+
DEEEIIHHKIJILKHLHIKEKHHMKLKKJGKKKKLKLFIHEKIKL=KLJLKIILHKMH9LJJ
@ERR162872.21706338/1:0:17:1:99
CTTCTTTGCA
+
BHBFH<EIFG
@ERR243039.1049231/2:0:17:1:163
TGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCA
+
AEEFIFHIJDGIGIJHHIAGGGLGJIEJHJHHFIJGJJDFJIG
@ERR013140.20277196/2:1:17:97:163
AAACTGTCCAGCGCATACCCGCATCCCCCCAAAAGAAGCCACCGCCCCAACACACACCCCCCACCCGCATAACC
+
00($,+3(*+..,%%+6%*#%2,/001)%%$2%%/$.%$00(,%+,1'*.%7(%&$&#'$$$#%#%#($+%+)"
@ERR013140.19887184/1:0:17:99:113
GTGTGTGTCGGGGGTGTCTGGGGTCTCACCCACGACCAAC
+
%$($&$*+#%%#1'$$%2-'0&3$/$/$-73/69:7=1%2
@ERR013140.4461044/1:0:17:114:113
ACTCCCTGGGCCTGGCA
+
/=1:/=44-348<0(91
@ERR013140.3521432/2:0:17:226:147
CACCCCTAGAAGTGACGGC
+
71%??A9A792/7-2%(&:
@ERR013140.11659627/1:0:17:645:83
TTAGCAACAAAAAGGAC
+
%5?-$)89<=;9>(.14
@ERR013140.7259970/1:0:17:660:83
ACGCCTGGTACA
+
40&/81&8:/<<
@ERR013140.29762488/1:0:17:716:83
GGACTCA
+
)/4/142
@ERR013140.11567710/1:0:17:984:83
TGCTTGA
+
/36>+5/

Cited In

• Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs : http://nar.oxfordjournals.org/content/44/21/10437.full
• Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences Nature Communicationsvolume 10, Article number: 3848 (2019) https://doi.org/10.1038/s41467-019-11658-z
• High-throughput Detection of T-DNA Insertion Sites for Multiple Transgenes in Complex Genomes. Edwards & al. Research Square. https://doi.org/10.21203/rs.3.rs-1325310/v1

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