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Picard SortSam error Unrecognized tag type
eeuzc
SwitzerlandMember ✭
I'm running several samples through a pipeline and using Picard 1.80 and Java version 1.7.0_51. Most of the samples are running fine but I got this error message for two of the samples: net.sf.samtools.SAMFormatException: Unrecognized tag type: # (the tag type was ^^ for another sample).
I'm using SORT_ORDER=coordinate. The bam file from the last step seems to be okay as seen with samtools flagstat. Is there any other way to check the inout bam file?
Searching online only gave "Unrecognized tag type: B", which seems to be resolved in Picard 1.5 version. So I don't know why I'm getting this error!
Answers
Hi Geraldine,
I tried to run this with Picard 2.2.1 (and Java 1.8) but I still get the same errors with these samples.
@eeuzc
Hi,
What happens if you run ValidateSamFile on those BAMs?
-Sheila