Commands reference

From PileLine

Revision as of 10:01, 24 June 2010 (view source) 127.0.0.1 (Talk) (→Analysis Commands) ← Older edit		Revision as of 10:09, 24 June 2010 (view source) 127.0.0.1 (Talk) (→Processing and Annotation Commands) Newer edit →
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	==Processing and Annotation Commands==		==Processing and Annotation Commands==
	*'''''pileline-fastseek.sh'''''		*'''''pileline-fastseek.sh'''''
-	Prints a given range of a locus file:	+	Prints a given range of a locus file.
-	pileline-fastseek.sh –p <locus_file.txt> -s chr10:100:10000	+
		+	'''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.sh –p <GP_file> -s chr10:100:10000
	*'''''pileline-fastsjoin.sh'''''		*'''''pileline-fastsjoin.sh'''''

---

Revision as of 10:09, 24 June 2010

Processing and Annotation Commands

• pileline-fastseek.sh

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.sh –p <GP_file> -s chr10:100:10000

• pileline-fastsjoin.sh

Joins two positional files:

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.

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

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.