jvarkit

Biostar489074

Last commit

call variants for every paired overlaping read

Usage

Usage: biostar489074 [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --maxRecordsInRam
      When writing  files that need to be sorted, this will specify the number 
      of records stored in RAM before spilling to disk. Increasing this number 
      reduces the number of file  handles needed to sort a file, and increases 
      the amount of RAM needed
      Default: 50000
    -o, --output
      Output file. Optional . Default: stdout
    --groupby, --partition
      Group Reads by. 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]
    --ploidy
      default ploidy
      Default: 2
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --regions
      Limit analysis to this interval. 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;,]'
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --version
      print version and exit

Keywords

See also in Biostars

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar489074

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

Creation Date

20200205

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar489074.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite biostar489074 ? 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

Description

input must be sorted on read name using samtools sort -n or ` samtools collate`

it will be much faster is the reads belong to one chromosome

Example

$ samtools view -O BAM --reference "ref.fasta" in.cram "chr22:41201525-41490147" |\
	samtools collate -O -u - |\
	java -jar dist/biostar489074.jar --reference "ref.fasta"