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# 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. | # 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. | # [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 | + | # Genotyping quality control functionality to estimate 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. |
==PileLine Commands== | ==PileLine Commands== | ||
Revision as of 17:45, 7 June 2010
Contents |
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 downloading 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 to estimate performance metrics (Harismendi et al. 2009) on detecting homo/heterozigote variants against a given gold standard genotype.
PileLine Commands
Processing Commands
- pileline-fastseek.sh
Prints a given range of a locus file.
- pileline-fastsjoin.sh
Joins two positional files.
- pileline-rfilter.sh
Filters (or annotates) a positional file with range-based annotations (in bed format). Each position that is inside of a specific range is annotated.
- pileline-genindex.sh
Indexes fasta genome and then can perform range based queries in that genome.
Analysis Commands
- pileline-2smc.sh
Looks for discrepancies in genotypes of two samples (i.e.: case vs control). It also can annotate each output position with a given positional file containing custom annotations (i.e. dbSNP). Also produces a SIFT and PolyPhen-2 compatible outfiles.
- pileline-nsmc.sh
Takes the output of several 2smc comparisons commands to reports where variants are reproduced.
- pileline-genotest.sh
Calculates the NGS performance on genotyping, surveying a set of genomic positions whose genotype is known in the sample.
Use Cases
- Annotate a locus file with dbSNP.
pileline-fastjoin.sh –a <locus_file.txt> -b dbSNP130.txt --left-outer-join
- Annotate a locus file with genes.
pileline-rfilter.sh --annotate –A <locus_file.txt> –b <genes.bed>
- Filter pileup to exon loci.
pileline-rfilter.sh –A <locus_file.txt> –b <exons.bed>
- Perform 2 samples comparison.
pileline-2smc.sh –a <locusfile_A.txt> –b <locusfile_B.txt> –v <variants_locusfile_A.txt> –w <variants__locusfile_B.txt> –o <out.txt> -d <min_depth>
- Perform n samples comparison.
pileline-nsmc.sh --a-samples<locusfile_a1>,<locusfile_a2>,<locusfile_a3> --b-samples <locusfile_b1>,<locusfile_b2>,<locusfile_b3>
- Perform a genotyping test for quality control.
pileline-genotest –p <locus_file.txt> –g <gold_genotype> -r <ref_genome.pileline> -t <snpq_treshold>
