[Samtools-help] MATE_NOT_FOUND after library filtering

[Hannes S. <hs...@sa...>]

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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