Use new script for checking Illumina data files
The picard program (see #631) mostly checks that data files exists and have a reasonable size. We have developed another script that also performs some basic checking of the correctness of the data files: /usr/local/packages/genseq_tools/v0.01/genseq_check_illumina_dir.pl
-t parameter is used to specify lane: -t 1, -t 1,2,5 (it can also be used to specify tiles but we are not interested in this)
-c parameter can be used to specify cycles to check. We can use this to skip checking cycles which are excluded by the read string.
Output is simple. If all checked are ok:
Format: bcl.bgzf - complete
If there are any problems:
Format: bcl+clocs - with errors Missing: L001/C101.1/s_1_1101.bcl Missing: L001/C102.1/s_1_1101.bcl Missing: L001/C103.1/s_1_1101.bcl Missing: L001/C104.1/s_1_1101.bcl