Main Page
From PileLine
(Difference between revisions)
(→Use Cases) |
|||
| Line 11: | Line 11: | ||
# [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 for estimating 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. | # Genotyping quality control functionality for estimating 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== | ||
| + | ===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> | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | ===Analysis Commads=== | ||
==Use Cases== | ==Use Cases== | ||
[[File:Figure_paper_Final.png|right|thumb|PileLine coupled to SAMtools]] | [[File:Figure_paper_Final.png|right|thumb|PileLine coupled to SAMtools]] | ||
Revision as of 16:15, 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 download 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
- 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>
Analysis Commads
Use Cases
