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From PileLine
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# [http://sift.jcvi.org/ SIFT] and [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] compatible outputs to facilitate the biological interpretation of huge lists of variants. | # [http://sift.jcvi.org/ SIFT] and [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] compatible outputs to facilitate the biological interpretation of huge lists of variants. | ||
# Genotyping quality control functionality for estimating performance metrics [http://www.ncbi.nlm.nih.gov/pubmed/19327155 (Harismendi et al. 2009)] on detecting homo/heterozigote variants against a given gold standard genotype. | # Genotyping quality control functionality for estimating performance metrics [http://www.ncbi.nlm.nih.gov/pubmed/19327155 (Harismendi et al. 2009)] on detecting homo/heterozigote variants against a given gold standard genotype. | ||
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| + | ==Use Cases== | ||
Revision as of 15:40, 7 June 2010
Welcome to PileLine 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. pileup files from SAMTools). PileLine is designed to be memory efficient by performing on-disk operations over sorted locus files directly.
PileLine is available for download at: http://sourceforge.net/projects/pileline
Main Features
- Filtering and comparison of locus text files.
- 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.
- SIFT and PolyPhen-2 compatible outputs to facilitate the biological interpretation of huge lists of variants.
- Genotyping quality control functionality for estimating performance metrics (Harismendi et al. 2009) on detecting homo/heterozigote variants against a given gold standard genotype.
