Hi,
SamToFastq.jar will be stop when it meet the unmapped reads which flag is 4 or 20 but the MAPQ is not 0. Picard is not so smart,it couldnot...
2 results in 0.0030 seconds.
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picard SamToFastq error in umapped reads which MAPQ is not 0
Last edited by upper; 12-05-2012, 05:33 PM. -
GATK "MAPQ should be 0 for unmapped read" complaint for mapped read
In running UnifiedGenotyper in GATK, I got the following error message:
Exception in thread "main" net.sf.samtools.SAMFormatException:...