Main Page
From PileLine
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| - | = Welcome to PileLine | + | = 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. [http://samtools.sourceforge.net SAMTools] [http://samtools.sourceforge.net/pileup.shtml pileup] files ). | 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. [http://samtools.sourceforge.net SAMTools] [http://samtools.sourceforge.net/pileup.shtml pileup] files ). | ||
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==Main Features== | ==Main Features== | ||
# Filtering and comparison of locus text files. | # Filtering and comparison of locus text files. | ||
| - | # Full annotation of locus files with human [http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP], [http://www.genenames.org/ HGNC] Gene Symbol and [http://www.ensembl.org/ Ensembl IDs]. Custom annotations are also allowed and may be supplied through standard . | + | # Full annotation of locus files with human [http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP], [http://www.genenames.org/ HGNC] Gene Symbol and [http://www.ensembl.org/ Ensembl IDs]. Custom annotations are also allowed and may be supplied through standard [http://genome.ucsc.edu/FAQ/FAQformat#format1 .BED] or [http://genome.ucsc.edu/FAQ/FAQformat#format3 .GFF] files. |
| - | # | + | # [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. | ||
Revision as of 15:15, 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. 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 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.
