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*Records to process
*Records to process
The <code>--first_n_record</code> option followed by a number, '''n''', will enable qplot to read the first '''n''' reads to test the bam files and verify it works.
The <code>--first_n_record</code> option followed by a number, '''n''', will enable qplot to read the first '''n''' reads to test the bam files and verify it works.
'''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 ":".
*Mapping filters
* Read group to process :
Read group option can restrict qplot to process a subset of reads. For example, if BAM contain the following @RG tags:
@RG ID:UM0348_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0348_2:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0348_3:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0348_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0360_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0360_2:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0360_3:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
@RG ID:UM0360_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
If specify nothing or not using "--readGroup", QPLOT by default will 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.
* 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.
However, you can force QPLOT to continue process using --noeof. But you should be award the input files may be corrupted.
* Mapping filters
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.
