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== Binary Download ==
== Binary Download ==
We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.20120602.tar.gz qplot.20120602.tar.gz (File Size: 1.7G)]
We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.20130619.tar.gz qplot.20130619.tar.gz (File Size: 1.7G)]
The executable file is under qplot/bin/qplot.
The executable file is under qplot/bin/qplot.
== Source Code Distribution ==
== Source Code Distribution ==
We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20120602.tar.gz qplot-source.20120602.tar.gz]. Optionally, you can download example file and/or data file:
We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20130619.tar.gz qplot-source.20130619.tar.gz]. Optionally, you can download example file and/or data file:
[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example | direction]].
[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example | direction]].
* 1. Unarchive downloaded file
* 1. Unarchive downloaded file
tar zvxf qplot-source.20120602.tar.gz
tar zvxf qplot-source.20130619.tar.gz
A new folder ''qplot'' will be created.
A new folder ''qplot'' will be created.
* 2. Build libStatGen
* 2. Build libStatGen
cd qplot
cd qplot
make libStatGen
(cd ../libStatGen; make cloneLib)
This step will download a necessary software library [http://genome.sph.umich.edu/wiki/C%2B%2B_Library:_libStatGen libStatGen] and compile source code into a binary code library.
This step will download a necessary software library [http://genome.sph.umich.edu/wiki/C%2B%2B_Library:_libStatGen libStatGen] and compile source code into a binary code library.
* 3. Build qplot
* 3. Build qplot
make all
make
This step will then build qplot. Upon success, the executable qplot can be found under qplot/bin/.
This step will then build qplot. Upon success, the executable qplot can be found under qplot/bin/.
some_linux_host > qplot/bin/qplot
some_linux_host > qplot/bin/qplot
The following parameters are available. Ones with "[]" are in effect:
References : --reference [/net/fantasia/home/zhanxw/software/qplot/data/human.g1k.v37.fa],
--dbsnp [/net/fantasia/home/zhanxw/software/qplot/data/dbSNP130.UCSC.coordinates.tbl]
GC content file options : --winsize [100]
Region list : --regions [], --invertRegion
Flag filters : --read1_skip, --read2_skip, --paired_skip,
--unpaired_skip
Dup and QCFail : --dup_keep, --qcfail_keep
Mapping filters : --minMapQuality [0.00]
Records to process : --first_n_record [-1]
Lanes to process : --lanes []
Read group to process : --readGroup []
Input file options : --noeof
Output files : --plot [], --stats [], --Rcode [], --xml []
Plot labels : --label [], --bamLabel []
Obsoleted (DO NOT USE) : --gccontent [], --create_gc
== Input files ==
== Input files ==
This file has two columns. First column is the chromosome name which must be consistent with the reference created above. Second column is 1-based SNP position. If you want to create your own dbSNP data from downloaded UCSC dbSNP file, one way to do it is: <code>cat dbsnp_129_b36.rod|grep "single" | awk '$4-$3==1' |cut -f2,4 > dbSNP_129_b36.tbl</code>
This file has two columns. First column is the chromosome name which must be consistent with the reference created above. Second column is 1-based SNP position. If you want to create your own dbSNP data from downloaded UCSC dbSNP file, one way to do it is: <code>cat dbsnp_129_b36.rod|grep "single" | awk '$4-$3==1' |cut -f2,4 > dbSNP_129_b36.tbl</code>
* <code>--gccontent</code>
* <code> **OBSOLETED** --gccontent, --create_gc </code>
Although GC content can be calculated on the fly each time, it is much more efficient to load a precomputed GC content from a file. To generate the file, use the following command:
Although GC content can be calculated on the fly each time, it is much more efficient to load a precomputed GC content from a file.
GC content file name is automatically determined in this format: <reference_genome_base_file_name>.winsize<gc_content_window_size>.gc.
For example, if your reference genome is human.g1k.v37.fa and the window size is 100, then the GC content file name is: human.g1k.v37.winsize100.gc .
As it said, there is no need to use --gccontent to specify GC content file in each run.
* <code> input files </code>
QPLOT take SAM/BAM files.
''Note'': Before running qplot, it is critical to check how the chromosome names are coded. Some BAM/SAM files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome names from the reference and dbSNP are consistent with the BAM/SAM files.'''
''Note'': Before running qplot, it is critical to check how the chromosome names are coded. Some BAM/SAM files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome names from the reference and dbSNP are consistent with the BAM/SAM files.'''
