PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files

PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files

1. Quick filtering and search within GP files without indexing steps.
2. GP files comparisons.
3. Full annotation of GP 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.
4. SIFT, PolyPhen-2 and Firestar compatible inputs to facilitate the biological interpretation of huge lists of variants.
5. Genotyping quality control functionality to estimate performance metrics (Harismendi et al. 2009) on detecting homo/heterozigote variants against a given gold standard genotype.
6. Modular design to facilitate the inclusion of new functionalities.