jvarkit

NgsFilesSummary

Scan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..). Useful to get a summary of your samples.

Usage

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

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

Usage: ngsfilessummary [options] Files
  Options:
    --format
      output format
      Default: tsv
      Possible Values: [tsv, xml]
    -header, --header
      [20180725]print header
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -i, --indexed
      [20190905]VCF or BAM must be indexed
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -p, --partition
      For BAM files: Data partitioning using the SAM Read Group (see 
      https://gatkforums.broadinstitute.org/gatk/discussion/6472/ ) . It can 
      be any combination of sample, library....
      Default: sample
      Possible Values: [readgroup, sample, library, platform, center, sample_by_platform, sample_by_center, sample_by_platform_by_center, any]
    -R, --reference
      [20190905]restrict to thoses reference(s). Also is used to read CRAM 
      files. A file with the '.list' suffix is interpreted as a list of paths 
      to fasta REF.
      Default: []
    --version
      print version and exit

Keywords

• sam
• bam
• vcf
• util

Creation Date

20140430

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/ngsfiles/NgsFilesSummary.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/ngsfiles/NgsFilesSummaryTest.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 ngsfilessummary ? 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 /projects/align01/ -type f |\
  java -jar dist/ngsfilessummary.jar 

SAMPLE1	BAM	/projects/align01/Samples/SAMPLE1/BAM/SAMPLE1_final.bam	321262321	Wed Jun 26 10:30:07 CEST 2013
SAMPLE1	FASTQ	/project/align01/fastq/SAMPLE1/SAMPLE1_CGATGT_L008_R1_002.fastq.gz	35828879	Fri Oct 18 16:15:58 CEST 2013
SAMPLE1	VCF	/projects/align01/Samples/SAMPLE1/VCF/SAMPLE1_variations.freebayes.vcf.gz	184191	Mon Jun 17 14:47:22 CEST 2013
SAMPLE1	VCF	/projects/align01/Samples/SAMPLE1/VCF/SAMPLE1_variations.gatk.vcf.gz	113341	Mon Jun 17 11:57:19 CEST 2013
SAMPLE1	VCF	/projects/align01/Samples/SAMPLE1/VCF/SAMPLE1_variations.samtools.vcf.gz	57518	Mon Jun 17 11:58:49 CEST 2013
SAMPLE2	BAM	/projects/align01/Samples/SAMPLE2/BAM/SAMPLE2_final.bam	286100773	Wed Jun 26 10:47:09 CEST 2013
SAMPLE2	FASTQ	/project/align01/fastq/SAMPLE2/SAMPLE2_CGATGT_L008_R1_002.fastq.gz	356828879	Fri Oct 18 16:15:58 CEST 2013
SAMPLE2	VCF	/projects/align01/Samples/SAMPLE2/VCF/SAMPLE2_variations.freebayes.vcf.gz	172970	Mon Jun 17 14:45:51 CEST 2013
SAMPLE2	VCF	/projects/align01/Samples/SAMPLE2/VCF/SAMPLE2_variations.gatk.vcf.gz	106390	Mon Jun 17 11:57:19 CEST 2013
SAMPLE2	VCF	/projects/align01/Samples/SAMPLE2/VCF/SAMPLE2_variations.samtools.vcf.gz	52709	Mon Jun 17 11:58:04 CEST 2013

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