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From PileLine
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# 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. | # 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 [http://www.ncbi.nlm.nih.gov/pubmed/19561590 (Kumar et al. 2009)] and PolyPhen [http://www.ncbi.nlm.nih.gov/pubmed/12202775 (Ramensky et al. 2002)] compatible outputs to facilitate the biological interpretation of huge lists of variants. | # SIFT [http://www.ncbi.nlm.nih.gov/pubmed/19561590 (Kumar et al. 2009)] and PolyPhen [http://www.ncbi.nlm.nih.gov/pubmed/12202775 (Ramensky et al. 2002)] 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. | + | # 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. |
Revision as of 15:03, 7 June 2010
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.
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 (Kumar et al. 2009) and PolyPhen (Ramensky et al. 2002) 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.
