Hello,
I have some .bam files that I want to filter to exclude reads from all but one
library.
I do this via:
samtools view -bh -l <libary_to_keep> <input.bam> > <output.bam>
However, when I run Picard ValidateSamFile.jar the original files don't show
any errors, but the resulting files show the error:
## HISTOGRAM java.lang.String
Error Type Count
ERROR:MATE_NOT_FOUND 106297180
Could anyone tell me why this is happening, whether this is a real problem and
what I could to against it?
I am using SAMtools/1.3.1
Many thanks,
Hannes
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