jvarkit

BamStats02

Statistics about the flags and reads in a BAM

Usage

Usage: bamstats02 [options] Files
  Options:
    -B, --bed
      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;,]' 
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -R, --ref
      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

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 bamstats02

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/bamstats01/BamStats02.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 bamstats02 ? 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

$  find dir -name "*final.bam" | xargs  java -jar dist/bamstats02.jar -B capture.bed  > output.tsv
$  verticalize output.tsv

>>> 2
$1      #filename       dir/Sample0258.final.bam
$2      sampleName      Sample0258
$3      chromosome      2
$4      mapq    60
$5      inTarget        1
$6      READ_PAIRED     1
$7      READ_MAPPED_IN_PROPER_PAIR      1
$8      READ_UNMAPPED   0
$9      MATE_UNMAPPED   0
$10     READ_REVERSE_STRAND     1
$11     MATE_REVERSE_STRAND     0
$12     FIRST_IN_PAIR   0
$13     SECOND_IN_PAIR  1
$14     NOT_PRIMARY_ALIGNMENT   0
$15     READ_FAILS_VENDOR_QUALITY_CHECK 0
$16     READ_IS_DUPLICATE       0
$17     SUPPLEMENTARY_ALIGNMENT 0
$18     count   463982
<<< 2

>>> 3


>>> 3
$1      #filename       dir/Sample0258.final.bam
$2      sampleName      Sample0258
$3      chromosome      .
$4      mapq    0
$5      inTarget        -1
$6      READ_PAIRED     1
$7      READ_MAPPED_IN_PROPER_PAIR      0
$8      READ_UNMAPPED   1
$9      MATE_UNMAPPED   1
$10     READ_REVERSE_STRAND     0
$11     MATE_REVERSE_STRAND     0
$12     FIRST_IN_PAIR   1
$13     SECOND_IN_PAIR  0
$14     NOT_PRIMARY_ALIGNMENT   0
$15     READ_FAILS_VENDOR_QUALITY_CHECK 0
$16     READ_IS_DUPLICATE       0
$17     SUPPLEMENTARY_ALIGNMENT 0
$18     count   458630
<<< 3

>>> 4
$1      #filename       dir/Sample0258.final.bam
$2      sampleName      Sample0258
$3      chromosome      .
$4      mapq    0
$5      inTarget        -1
$6      READ_PAIRED     1
$7      READ_MAPPED_IN_PROPER_PAIR      0
$8      READ_UNMAPPED   1
$9      MATE_UNMAPPED   1
$10     READ_REVERSE_STRAND     0
$11     MATE_REVERSE_STRAND     0
$12     FIRST_IN_PAIR   0
$13     SECOND_IN_PAIR  1
$14     SECONDARY_ALIGNMENT   0
$15     READ_FAILS_VENDOR_QUALITY_CHECK 0
$16     READ_IS_DUPLICATE       0
$17     SUPPLEMENTARY_ALIGNMENT 0
$18     count   458630
<<< 4

```

See also

BamStats02View

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