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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 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
- Prints a given range of a locus file:
- pileline-fastsjoin.sh
- Joins two positional files:
- i.e. XXXXX
- 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.
- 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>
- 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.
- i.e. pileline-genindex –-index –g <fasta> -i <new_index>
- i.e. pileline-genindex --seek –i <index> -s chr1:1000:2000
- 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
