Changes

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 :  

Read group option can restrict qplot to process a subset of reads. For example, if BAM contain the following @RG tags:

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

If specify nothing or not using "--readGroup", QPLOT by default will process all reads;

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 :

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