This is the command rabema_build_gold_standard that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
rabema_build_gold_standard - RABEMA Gold Standard Builder
SYNOPSIS
rabema_build_gold_standard [OPTIONS] --out-gsi OUT.gsi --reference REF.fa --in-sam
PERFECT.sam rabema_build_gold_standard [OPTIONS] --out-gsi OUT.gsi --reference
REF.fa --in-bam PERFECT.bam
DESCRIPTION
This program allows to build a RABEMA gold standard. The input is a reference FASTA
file and a perfect SAM/BAM map (e.g. created using RazerS 3 in full-sensitivity
mode).
The input SAM/BAM file must be sorted by coordinate. The program will create a
FASTA index file REF.fa.fai for fast random access to the reference.
-h, --help
Displays this help message.
--version
Display version information
-v, --verbose
Enable verbose output.
-vv, --very-verbose
Enable even more verbose output.
Input / Output:
-o, --out-gsi GSI
Path to write the resulting GSI file to. Valid filetypes are: gsi and gsi.gz.
-r, --reference FASTA
Path to load reference FASTA from. Valid filetypes are: fa and fasta.
-s, --in-sam SAM
Path to load the "perfect" SAM file from. Valid filetype is: sam.
-b, --in-bam BAM
Path to load the "perfect" BAM file from. Valid filetype is: bam.
Gold Standard Parameters:
--oracle-mode
Enable oracle mode. This is used for simulated data when the input SAM/BAM file
gives exactly one position that is considered as the true sample position.
--match-N
When set, N matches all characters without penalty.
--distance-metric METRIC
Set distance metric. Valid values: hamming, edit. Default: edit. One of hamming and
edit. Default: edit.
-e, --max-error RATE
Maximal error rate to build gold standard for in percent. This parameter is an
integer and relative to the read length. In case of oracle mode, the error rate for
the read at the sampling position is used and RATE is used as a cutoff threshold.
Default: 0.
RETURN VALUES
A return value of 0 indicates success, any other value indicates an error.
EXAMPLES
rabema_build_gold_standard -e 4 -o OUT.gsi -s IN.sam -r REF.fa
Build gold standard from a SAM file IN.sam with all mapping locations and a FASTA
reference REF.fa to GSI file OUT.gsi with a maximal error rate of 4.
rabema_build_gold_standard --distance-metric edit -e 4 -o OUT.gsi -b IN.bam -r
REF.fa
Same as above, but using Hamming instead of edit distance and BAM as the input.
rabema_build_gold_standard --oracle-mode -o OUT.gsi -s IN.sam -r REF.fa
Build gold standard from a SAM file IN.sam with the original sample position, e.g.
as exported by read simulator Mason.
MEMORY REQUIREMENTS
From version 1.1, great care has been taken to keep the memory requirements as low
as possible. There memory required is two times the size of the largest chromosome
plus some constant memory for each match.
For example, the memory usage for 100bp human genome reads at 5% error rate was
1.7GB. Of this, roughly 400GB came from the chromosome and 1.3GB from the matches.
REFERENCES
M. Holtgrewe, A.-K. Emde, D. Weese and K. Reinert. A Novel And Well-Defined
Benchmarking Method For Second Generation Read Mapping, BMC Bioinformatics 2011,
12:210.
http://www.seqan.de/rabema
RABEMA Homepage
http://www.seqan.de/mason
Mason Homepage
VERSION
rabema_build_gold_standard version: 1.2.0 Last update March 14, 2013
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