Dear developers!
The headers of the mapped bam files produced by the latest version of gemBS (gemBS 3.5.5) contain a SM key without value. This causes problems in various tools, for example picard MarkDuplicates (https://broadinstitute.github.io/picard/). This can easily be circumvented by adding a placeholder value (SM:placeholder), nevertheless it would probably be nice to not have to do this kind of extra reheadering, hence I wanted to draw your attention to this issue.
All the best,
Nikolaus
To generate the error (in the directory where picard.jar is located):
java -jar picard.jar MarkDuplicates I=test.bam O=test_deduped.bam M=marked_dup_metrics.txt REMOVE_DUPLICATES=true
Dear developers!
The headers of the mapped bam files produced by the latest version of gemBS (gemBS 3.5.5) contain a SM key without value. This causes problems in various tools, for example picard MarkDuplicates (https://broadinstitute.github.io/picard/). This can easily be circumvented by adding a placeholder value (SM:placeholder), nevertheless it would probably be nice to not have to do this kind of extra reheadering, hence I wanted to draw your attention to this issue.
All the best,
Nikolaus
To generate the error (in the directory where picard.jar is located):
java -jar picard.jar MarkDuplicates I=test.bam O=test_deduped.bam M=marked_dup_metrics.txt REMOVE_DUPLICATES=true