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|[[File:genome_browser.png|thumb|PileLine GUI's interactive genome browser.]]  
|[[File:genome_browser.png|thumb|PileLine GUI's interactive genome browser.]]  
|[[File:gpfiles_view.png|thumb|PileLine GUI showing a instantly-navigable .pileup file.]]
|[[File:gpfiles_view.png|thumb|PileLine GUI showing a instantly-navigable .pileup file.]]
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|}
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You can get sample files to test PileLine GUI in our [[Sample_Data|Sample data]]. The following table shows which files are required for which functionality:
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{| border="1" cellspacing="0" cellpadding="2"
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|-align="left"
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!scope="col"| Functionality
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!scope="col"| Files
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!scope="col"| Description
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|-align="left"
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!scope="row"| Somatic mutation calling
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(2-smc and n-smc)
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|
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[[Media:Control1Files.zip|Control1Files.zip]] (36MB)
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[[Media:Case1Files.zip|Case1Files.zip]] (36MB)
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[[Media:Control2Files.zip|Control2Files.zip]] (38MB)
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[[Media:Case2Files.zip|Case2Files.zip]] (38MB)
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| For 2-smc you need at least Control1 and Case1 files. For n-smc, you need all.
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'''NOTE: This files have only information for the chromosome 10'''
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|-align="left"
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!scope="row"| Filter and annotation
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|
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[[Media:DbSNP_36.3.txt.zip|DbSNP_36.3.txt.zip]] (237MB)
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[[Media:Hg18_hgnc_ensembl_genes.bed.zip|Hg18_hgnc_ensembl_genes.bed.zip]] (365KB)
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| You need at least the genome file. In order to add tracks, you need GP files.
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|-align="left"
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!scope="row"| Genome Browser
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| [http://sing.ei.uvigo.es/pileline/data/hg18.tar.gz hg18.tar.gz] (892MB)
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| You need at least the genome file. In order to add tracks, you need GP files.
|}
|}

Revision as of 12:26, 4 January 2011

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/

PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser.

Main Features

PileLine commands and accepted input files.
  1. Quick filtering and search within GP files without indexing steps.
  2. GP files comparisons.
  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.
  6. Modular design to facilitate the inclusion of new functionalities.

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-fastjoin

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-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. This functionality requires a previous step using *pileline-genindex command for genome indexing.

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
Genotest metrics table description. It may be obtained by using --print-help-table argument.
# 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 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

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

PileLine GUI

PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser. With this intuitive graphical desktop application you can run the following tasks:

  1. Processing commands of GP files, like seek, join, annotate and filtering.
  2. Perform 2-samples and n-samples point somatic mutation calling (via the PileLine 2smc and nsmc commands).
  3. Browse GP files in a interactive local genome browser.

You can download PileLine GUI from Downloads.

General scheme of the PileLine GUI software.
PileLine GUI's interactive genome browser.
PileLine GUI showing a instantly-navigable .pileup file.

You can get sample files to test PileLine GUI in our Sample data. The following table shows which files are required for which functionality:

Functionality Files Description
Somatic mutation calling

(2-smc and n-smc)

Control1Files.zip (36MB)

Case1Files.zip (36MB)

Control2Files.zip (38MB)

Case2Files.zip (38MB)

For 2-smc you need at least Control1 and Case1 files. For n-smc, you need all.

NOTE: This files have only information for the chromosome 10

Filter and annotation

DbSNP_36.3.txt.zip (237MB)

Hg18_hgnc_ensembl_genes.bed.zip (365KB)

You need at least the genome file. In order to add tracks, you need GP files.
Genome Browser hg18.tar.gz (892MB) You need at least the genome file. In order to add tracks, you need GP files.
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