[Samtools-devel] DownsampleSam and Supplementary Reads

[Martin P. <mp...@sa...>]

Hi,

At the moment Picard’s DownsampleSam seems to be dropping all supplementary reads.  This does not seem like correct behaviour, given that these reads contain key information about the primary alignment.  One could probably make a similar argument about Secondary mappings too.

I’ve traced the removal to this line:
https://github.com/broadinstitute/picard/blob/master/src/java/picard/sam/DownsampleSam.java#L65
Would the Picard developers be amenable to a patch that either removes this line or makes it a non-default option?

Martin

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