Commands reference

From PileLine

Revision as of 10:47, 24 June 2010

Processing and Annotation Commands

• pileline-fastseek

Prints a given range of a locus file.

Usage: pileline-fastseek -p <GP_file> -s <range> [--seq-col <int>] [--pos-col <int>]

Option                                  Description                            
------                                  -----------                            
-p, --gp-file <File>                    SORTED genome position file to seek  [required]                           
--pos-col <Integer>                     position column for the gp-file. The first is 1 (default: 2)              
-s                                      seek position in the form of seq:start[:end] [required]             
--seq-col <Integer>                     sequence column for gp-file. The first is 1 (default: 1)

Example:

pileline-fastseek –p <GP_file> -s chr10:100:10000

• pileline-fastsjoin

Joins two positional files.

Usage: 
pileline-fastjoin.sh -a <left_file> -b <right_file> [--right-outer-join | --left-outer-join][--noprint-a | --noprint-b][--seq-col-a <int>][--pos-col-a <int>][--seq-col-b <int>][--pos-col-b <int>]

Option                                  Description                            
------                                  -----------                            
-a, --left-file <File>                 left tab-delimited AND SORTED genome position file [required]             
-b, --right-file <File>                right tab-delimited AND SORTED genome position file [required]             
--left-outer-join                      performs a left outer join: all A records will be in output, inexistent B records are showed by a NULL                                 
--noprint-a                            prints only data fields of A           
--noprint-b                            prints only data fields of B           
--pos-col-a <Integer>                  position column for the left file. The first is 1 (default: 2)              
--pos-col-b <Integer>                  position column for the right file. The first is 1 (default: 2)          
--right-outer-join                     performs a right outer join: all B records will be in output,  inexistent A records are showed as   NULL                                 
--seq-col-a <Integer>                  sequence column for the left file. The first is 1 (default: 1)              
--seq-col-b <Integer>                  sequence column for the right file. The first is 1 (default: 1)

Example:

pileline-fastjoin –a <GP_file> -b <GP_file>           

• 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.

Usage: 
pileline-rfilter [--annotate] -A <GP_file> [-b <bed> | -g <gff> | -i <intervals_file>] [-w <int>] [--seq-pos-input <int>] [--pos-col-input <int>] 
                 [--seq-col-intervals <int>] [--start-col-intervals <int>] [--end-col-intervals <int>]

Option                                  Description                            
------                                  -----------                            
-A, --input-file                        SORTED genome position file. Use - for stdin [required]                     
--annotate                              Do not filter. Annotate the lines with the ranges (last column)             
-b, --intervals-bed-file <File>         intervals file in BED format [required -b or -g]                            
--end-col-intervals <Integer>           end position column in the intervals file. The first is 1 (default: 3)    
-g, --intervals-gff-file <File>         intervals file in GFF format [required -b or -g]                            
-i, --intervals-gp-file <File>          intervals file in any other format     
--pos-col-input <Integer>               position column in the input file. The first is 1 (default: 2)              
--seq-col-input <Integer>               sequence column in the input file. The first is 1 (default: 1)              
--seq-col-intervals <Integer>           sequence column in the intervals file. The first is 1 (default: 1)          
--start-col-intervals <Integer>         start position column in the intervals file. The first is 1 (default: 2)    
-w, --window <Integer>                  expand each interval with <window> size at both sides (default: 0)

Example

pileline-rfilter –A <GP_file.txt> –i <targets.bed> 
pileline-rfilter --annotate –A <GP_file.txt> –i <annotations.bed> 

• pileline-genindex.sh

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

pileline-genindex –-index –g <fasta> -i <new_index>
pileline-genindex --seek –i <index> -s chr1:1000:2000

• pileline-pileup2sift.sh

Generates a SIFT-compatible change column for each variant line in the GPF.

pileline-pileup2sift -i <pileup> 
#Use - for STDIN.

• pileline-pileup2polyphen.sh

Generates a Polyhen-compatible change column for each variant line in the GPF.

pileline-pileup2polyphen -i <pileup> 
#Use - for STDIN.

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 user provided BED file containing custom annotations.

• 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.