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  • BMC Bioinformatics: PileLine toolbox to handle genome-position files in NGS studies.

    Link to the article in BMC Bioinformatics:
    Background Genomic position (GP) files currently used in next-generation sequencing (NGS) studies are always difficult to manipulate due to their huge size and the lack of appropriate tools to properly manage them. The structure of these flat files is based on representing one line per position that has been covered by at least one aligned read, imposing significant restrictions from a computational performance perspective. Results PileLine implements a flexible command-line toolkit providing specific support to the management, filtering, comparison and annotation of GP files produced by NGS experiments. PileLine tools are coded in Java and run on both UNIX (Linux, Mac OS) and Windows platforms. The set of tools comprising PileLine are designed to be memory efficient by performing fast seek on-disk operations over sorted GP files. Conclusions Our novel toolbox has been extensively tested taking into consideration performance issues. It is publicly available at http://sourceforge.net/projects/pilelinetools under the GNU LGPL license. Full documentation including common use cases and guided analysis workflows is available at http://sing.ei.uvigo.es/pileline .


    PileLine is publicly available at http://sourceforge.net/projects/pilelinetools under the GNU LGPL license.

    Full documentation including common use cases and guided analysis workflows is available at http://sing.ei.uvigo.es/pileline.
    Last edited by gonvader; 02-11-2011, 04:44 AM.

  • #2
    So can this annotate a VCF file with dbSNP in the ID field?

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    • #3
      PileLine annotates .vcf with dbSNP, however the novel SNPs annotation will be added in the last column of the output file (not in the vcf ID column). Of course if you have already SNP annotation in the ID column of your .vcf, PileLine will add novel annotation (provided by the user i.e. bed file) in the last column of the output file keeping the original annotation in the ID column.
      Last edited by gonvader; 02-10-2011, 06:02 AM.

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