I have tried the most current version of picard as well, but seem to have the same issue. When I run IlluminaBasecallstoFastq, with read-format as casava_1_8, I get nice fastq files with proper headers, but, almost all of the reads are labelled "Y" for pass-filter failed or not. I see from the QC metrics that most of the reads passed filter, so why picard is labeling them as failed filter. I think "Y" stands for failed filter and "N" stands for not failed filter, at least thats what it says here http://en.wikipedia.org/wiki/FASTQ_format "Y if the read is filtered, N otherwise"
Can anybody help me out to sort the problem? Thanks ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
