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call variants for every paired overlaping read


Usage: biostar489074 [options] Files
      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 MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
      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]
      default ploidy
      Default: 2
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
      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;,]'
      tmp working directory. Default: java.io.tmpDir
      Default: []
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
      print version and exit


See also in Biostars


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


Source code




The project is licensed under the MIT license.


Should you cite biostar489074 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:


Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030


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


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