Main Page
From PileLine
(Difference between revisions)
(→PileLine Commands) |
(→PileLine Commands) |
||
| Line 14: | Line 14: | ||
==PileLine Commands== | ==PileLine Commands== | ||
===Processing Commands=== | ===Processing Commands=== | ||
| - | *''pileline-fastseek.sh'' | + | *'''''pileline-fastseek.sh''''' |
::Prints a given range of a locus file: | ::Prints a given range of a locus file: | ||
| - | ::i.e. ''pileline-fastseek.sh'' –p <locus_file.txt> -s chr10:100:10000 | + | :::i.e. ''pileline-fastseek.sh'' –p <locus_file.txt> -s chr10:100:10000 |
| - | *''pileline-fastsjoin.sh'' | + | *'''''pileline-fastsjoin.sh''''' |
::Joins two positional files: | ::Joins two positional files: | ||
| - | ::i.e. XXXXX | + | :::i.e. XXXXX |
| - | *''pileline-rfilter.sh'' | + | *'''''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. | ::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'' –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> | + | :::i.e. ''pileline-rfilter'' --annotate –A <locus_file.tx> –i <annotations.bed> –o <out.txt> |
| - | *''pileline-genindex.sh'' | + | *'''''pileline-genindex.sh''''' |
::Indexes fasta genome and then can perform range based queries in that genome. | ::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'' –-index –g <fasta> -i <new_index> |
| - | ::i.e. ''pileline-genindex'' --seek –i <index> -s chr1:1000:2000 | + | :::i.e. ''pileline-genindex'' --seek –i <index> -s chr1:1000:2000 |
===Analysis Commands=== | ===Analysis Commands=== | ||
| - | *''pileline-2smc.sh'' | + | *'''''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. | ::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'' | + | *'''''pileline-nsmc.sh''''' |
::Takes the output of several 2smc comparisons commands to reports where variants are reproduced. | ::Takes the output of several 2smc comparisons commands to reports where variants are reproduced. | ||
| - | *''pileline-genotest.sh'' | + | *'''''pileline-genotest.sh''''' |
::Calculates the NGS performance on genotyping, surveying a set of genomic positions whose genotype is known in the sample. | ::Calculates the NGS performance on genotyping, surveying a set of genomic positions whose genotype is known in the sample. | ||
Revision as of 16:29, 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 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
