Commands reference
From PileLine
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| - | pileline-2smc -a <pileup> -b <pileup> --variants-a <pileup> --variants-b <pileup> --annotate < | + | pileline-2smc -a <pileup> -b <pileup> --variants-a <pileup> --variants-b <pileup> --annotate <bed> -d 30 |
Revision as of 11:34, 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)
Examples:
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.
Usage: pileline-genindex [OPTIONS] Option Description ------ ----------- -g, --genome-file <File> genome file to index in one unique fasta (on index mode) [required in --index] -i, --index-file <File> index file to create (on index mode) or to access (on seek mode) [required] --index Index mode -s Seek position in the form of seq:start[:end] [required] --seek Seek mode [default if no --index]
Examples:
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 pileup files.
Usage: pileline-pileup2sift -i <pileup> Option Description ------ ----------- -i, --pileup-file variants pileup (pileup -c) file to annotate. Use - for stdin.
Example:
pileline-pileup2sift -i <pileup_file>
- pileline-pileup2polyphen.sh
Generates a Polyhen-compatible change column for each variant line in pileup files.
Usage: pileline-pileup2polyphen -i <pileup> Option Description ------ ----------- -i, --pileup-file variants pileup (pileup -c) file to annotate. Use - for stdin.
Example:
pileline-pileup2polyphen -i <pileup_file>
Analysis Commands
- pileline-2smc.sh
Looks for discrepancies in genotypes of two samples (i.e.: case vs control) in pileup format files. It also can annotate each output position with a user provided BED file containing custom annotations.
Usage: pileline-2smc -a <pileup> -b <pileup> --variants-a <pileup> --variants-b <pileup> [OPTIONS] Option Description ------ ----------- --AdiscrepantB Calculate variants present in sample A (-v) and in sample B (-w), but with different genotype -a, --genotype-a <File> Whole genotype pileup (with MAQ consensus) file of sample A [required] --all Calculate all mutations (onlyA, onlyB, AdiscrepantB and both) [default] --annotate <File> Annotated positions with those of the provided BED file -b, --genotype-b <File> Whole genotype pileup (with MAQ consensus) file of sample B [required] --both Calculate variants present in sample A (-v) and in sample B (-w) and with the same genotype --cq-column <Integer> MAQ consensus quality column in variants and genotype files (default: 5) -d, --genotype-depth-filter-threshold genotype depth filter threshold <Integer>(default: 10) -o, --out-prefix <File> Output files prefix [required] --onlyA Calculate mutations which are variants in sample A (-v) and are homozigous-reference in B --onlyB Calculate mutations which are variants in sample B (-w) and are homozigous- reference in A -r, --reference-column <Integer> reference genotype column in genotype files (options -a and -b) (default:3) -t, --genotype-depth-filter-column genotype depth column (default: 8) <Integer> -v, --variants-a <File> Variants of interest in pileup format (with MAQ consensus) of sample A [required] -w, --variants-b <File> Variants of interest in pileup format (with MAQ consensus) of sample B [required]
Example:
pileline-2smc -a <pileup> -b <pileup> --variants-a <pileup> --variants-b <pileup> --annotate <bed> -d 30
- 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.
