jvarkit

BamForIndexCov

prepare BAM/CRAM from indexcov.

DEPRECATED

can be replace with samtools view. See doc

Usage

Usage: java -jar dist/bam4indexcov.jar  [options] Files
Usage: bam4indexcov [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -i, --include-chromosomes
      regex of chromosomes to only include
      Default: (chr)?[0-9XY]+
    -m, --manifest
      manifest file
    -Q, --mapq
      min mapping quality.
      Default: 10
    --md5
      generate md5 file
      Default: false
  * -o, --output
      Output directory
    -p, --prefix
      File prefix
      Default: bam4indexcov.
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --version
      print version and exit

Keywords

• cnv
• duplication
• deletion
• sv

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 bam4indexcov

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

Creation Date

20220506

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/indexcov/BamForIndexCov.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 bam4indexcov ? 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

DEPRECATED

can be replaced with

samtools view -F 3844 -q 30 -O BAM -o "/dev/null##idx##out.bam.bai" --write-index in.bam

example

``` java -jar dist/bam4indexcov.jar -R src/test/resources/rotavirus_rf.fa -o . src/test/resources/S.bam -i ‘RF1.’

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