From PileLine

Welcome to PileLine toolbox Wiki

PileLine (Pileup pipeLine) is a flexible command-line toolkit for efficient handling, filtering, and comparison of locus text files produced by next-generation sequencing experiments (i.e. SAMTools pileup files ). PileLine is designed to be memory efficient by performing on-disk operations over sorted locus files directly.

Main Features

i) Filtering and comparison of locus text files.

ii) Full annotation of locus files with human dbSNP, HGNC Gene Symbol and Ensembl IDs. Custom annotations are also allowed and may be supplied through standard .bed or .gff files.

iii) SIFT (Kumar et al. 2009) and PolyPhen (Ramensky et al. 2002) compatible outputs to facilitate the biological interpretation of huge lists of variants.

iv) Genotyping quality control functionality for estimating performance metrics (Harismendi et al. 2009) on detecting homo/heterozigote variants against a given gold standard genotype.

PileLine is available for download at: http://sourceforge.net/projects/pileline