From PileLine

Revision as of 16:19, 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. 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

1. Filtering and comparison of locus text files.
2. 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.
3. SIFT and PolyPhen-2 compatible outputs to facilitate the biological interpretation of huge lists of variants.
4. Genotyping quality control functionality for estimating 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:

i.e. pileline-fastseek.sh –p <locus_file.txt> -s chr10:100:10000

• pileline-fastsjoin.sh

Joins two positional files:

i.e. XXXXX

• 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.

i.e. pileline-rfilter –A <locus_file.txt> –i <targets.bed> –o <out.txt>

i.e. pileline-rfilter --annotate –A <locus_file.tx> –i <annotations.bed> –o <out.txt>

• pileline-genindex.sh

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

i.e. pileline-genindex –-index –g <fasta> -i <new_index>

i.e. pileline-genindex --seek –i <index> -s chr1:1000:2000

Analysis Commands

Use Cases

PileLine coupled to SAMtools