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[[File:Glez_Peña_et_al_Figure2.png|right|thumb|PileLine commands and accepted input files.]]
[[File:Glez_Peña_et_al_Figure2.png|right|thumb|PileLine commands and accepted input files.]]
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# Filtering and comparison of GP files.
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# Quick filtering and search within GP files.
 +
# N GP files comparison.
# Full annotation of GP 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 GP 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], [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] and [http://ubio.bioinfo.cnio.es/inb/firestar/firestar_batch/firestar.html Firestar] compatible inputs to facilitate the biological interpretation of huge lists of variants.  
# [http://sift.jcvi.org/ SIFT], [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] and [http://ubio.bioinfo.cnio.es/inb/firestar/firestar_batch/firestar.html Firestar] compatible inputs to facilitate the biological interpretation of huge lists of variants.  

Revision as of 08:50, 1 September 2010

Contents

Welcome to PileLine Wiki

PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments (i.e. pileup, BED,GFF, or VCF files). PileLine is designed to be memory efficient by performing on-disk operations over sorted GP files directly.

PileLine is available for downloading at: http://sourceforge.net/projects/pilelinetools/

Main Features

PileLine commands and accepted input files.
  1. Quick filtering and search within GP files.
  2. N GP files comparison.
  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.

.

Getting started

New to PileLine? Please, follow our Quick Start.

PileLine Commands

Processing and Annotation Commands

  • pileline-fastseek

Prints a given range of a GP file.

  • pileline-sort

Sorts GP files by coordinate.

  • pileline-fastsjoin

Joins two SORTED GP files.

  • pileline-rfilter

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

Indexes fasta genome and then can perform range based queries in that genome.

  • pileline-pileup2sift

Generates SIFT compatible infiles from pileup files.

  • pileline-pileup2polyphen

Generates PolyPhen-2 compatible infiles from pileup files.

  • pileline-pileup2firestar

Generates Firestar compatible infiles from GP files.

Analysis Commands

  • pileline-2smc

Looks for discrepancies in genotypes of two samples (i.e.: case vs control). It also can annotate each output position with a user provided BED file containing custom annotations.

  • pileline-nsmc

Compares n samples reporting consistent variants.

  • pileline-genotest

Calculates the NGS performance on genotyping, surveying a set of genomic positions whose genotype is known in the sample.

Use Cases

PileLine coupled to SAMtools facilitating pileup handling. NS: non-synonymous
  • Perform 2 samples comparison 
pileline-2smc.sh 
–a <file_A.pileup> –b <file_B.pileup>
–v <variants_file_A.pileup> –w <variants_file_B.pileup> 
–o <out.txt> -d <min_depth>
  • Perform n samples comparison 
pileline-nsmc.sh
--a-samples<GPfile_a1>,<GPfile_a2>,<GPfile_a3> 
--b-samples <GPfile_b1>,<GPfile_b2>,<GPfile_b3>
  • Sort GP files 
pileline-sort.sh -i <input_GP_file.txt> -o <outfile.sorted.txt>
  • Annotate a GP file with dbSNP 
pileline-fastjoin.sh –a <GP_file.txt> -b dbSNP130.txt --left-outer-join
  • Annotate a GP file with genes 
pileline-rfilter.sh --annotate –A <GP_file.txt> –b <genes.bed>
  • Filter pileup to exon loci 
pileline-rfilter.sh –A <GP_file.txt> –b <exons.bed>
  • Generate column compatible to SIFT intput 
pileline-pileup2sift.sh -i <file.pileup>
  • Perform a genotyping test for quality control 
# Warning: Check that your alleles in the <gold_genotype.sorted> file are expressed in the same strand as the 
#          reference genome sequence used in your NGS experiment. Typically forward (+) strand. 

## Step1.

#Create reference index <ref_genome.pileline> using pileline-genindex command.
pileline-genindex --index -i  <ref_genome.pileline> -g <ref_genome.fa>

## Step2.
#Create genotest file (required).
pileline-genotest --create-genotest-file <experiment.genotest> –p <GP_file.txt> –g <gold_genotype.sorted> -r <ref_genome.pileline>

## Step3. QC analysis.

#Generate a metrics table of performance at a given threshold.
pileline-genotest -a <experiment.genotest> -t <snpq_treshold>

#Generate all performance metrics for several thresholds
pileline-genotest -a <experiment.genotest> --batch-t 0,255,1

#Generate values for ROC curve plot (outfile compatible to ROCR R package)
pileline-genotest -a <experiment.genotest> --roc
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