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

[gonvader]

Link to the article in BMC Bioinformatics:

http://www.biomedcentral.com/1471-2105/12/31

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.

[trickytank]

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

[gonvader]

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.