jvarkit

BWAMemDigest

Usage

Usage: bwamemdigest [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --version
      print version and exit
    -B
      BED of Regions to ignore.
    -x
       Extend BED Regions to ignore by 'x' bases.
      Default: 0

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 bwamemdigest

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/mem/BWAMemDigest.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 bwamemdigest ? 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

package/bwa/bwa-0.7.4/bwa mem
-M ~/tmp/DATASANGER/hg18/chr1.fa
~/tmp/DATASANGER/4368_1_1.fastq.gz ~/tmp/DATASANGER/4368_1_2.fastq.gz 2> /dev/null | java -jar dist/bwamemdigest.jar -B <(curl -s “http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz” | gunzip -c | cut -f2,3,4 ) -x 500 | tee /dev/tty | gzip –best > /tmp/jeter.mem.bed.gz

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