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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.20130627.tar.gz qplot.20130627.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://csg.sph.umich.edu//zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.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.20130627.tar.gz qplot-source.20130627.tar.gz]. Optionally, you can download example file and/or data file:
We provide a source code only download in [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-source.20130627.tar.gz qplot-source.20130627.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://csg.sph.umich.edu//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-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100.
[http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100.
You can put above file(s) in the same folder and follow these steps:
You can put above file(s) in the same folder and follow these steps:
or
or
--qcfail_keep
--qcfail_keep
*Records to process
*Records to process
'''NOTE''' In order for this to work, the lane info has to be encoded in the read name such that the lane number is the second field with the delimiter ":".
'''NOTE''' In order for this to work, the lane info has to be encoded in the read name such that the lane number is the second field with the delimiter ":".
* Read group to process :
* Read group to process :
The read group option can restrict qplot to process a subset of reads. For example, if the BAM contains the following @RG tags:
@RG ID:UM0348_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0348_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0360_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0360_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
QPLOT will by default (without specifying --readgroup) process all reads.
If specify "--readGroup UM0348", then only read group UM0348_1, UM_0348_2, UM_0348_3, UM_0348_4 will be processed;
If specify "--readGroup UM0348_1", then only one read group UM0348_1 will be processed.
If you specify "--readGroup UM0348", then only read groups UM0348_1, UM_0348_2, UM_0348_3, UM_0348_4 will be processed.
If you specify "--readGroup UM0348_1", then only one read group, UM0348_1, will be processed.
* Input file options :
* Input file options :
BAM files are compress by BGZF algorithm and it should contain EOF by default. QPLOT will by default stop working when it does not found a valid EOF tag inside BAM files.
BAM files are compressed using BGZF and should contain the EOF indicator by default. QPLOT will, by default, stop working if it does not find a valid EOF indicator inside the BAM files.
However, you can force QPLOT to continue process using --noeof. But you should be aware the input files may be corrupted.
However, you can force QPLOT to continue processing BAM files without an EOF indicator using --noeof. But you should be aware the input files may be corrupted.
Qplot will exclude reads with lower mapping qualities than the user specified parameter, <code>--minMapQuality</code>. By default, mapped reads with all mapping quality will be included in the analysis.
Qplot will exclude reads with lower mapping qualities than the user specified parameter, <code>--minMapQuality</code>. By default, mapped reads with all mapping quality will be included in the analysis.
*Region list
*Region list
