myourshaw
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After further investigation, it appears that the problem may have been introduced between GATH 4.2.1.0 and 4.2.2.0, contrary to our original suspicion that it was introduced in 4.1.3.0. After gathe...
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This problem appears to be a bug in the version of Picard that is contained in GATK 4.2.0.0. When will GATK be updated with this fix? "This bug has been fixed in Picard release https://github.com/b...
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Additional information. I tried to demultiplex the same data with IlluminaBaseCallsToFastq, which had the same falure to demultiplex. All reads were in the UNKNOWN fastq files. No reads were in any...
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My guess is that the problem starts with IlluminaBaseCallsToSam. And the problem is with matching the barcodes in the BASECALS_DIR/BARCODES_DIR with those in the LibraryParams.