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Using Picard FilterSamReads with Java filters

I'm planning to use Picard FilterSamReads with FILTER=includeJavascript for some of my bamouts with --emitDroppedReads, and, to be frank, I still have no idea as for how that Javascript works. For example, if I use a script like this to identify reads that are not dropped by the caller:

function filterEmittedDroppedReads (record) { var ft = record.getAttribute("FT"); if (ft==null) { return true; }else { return false; } }

Yet FilterSamReads reports 0 reads passed the filter. I'm quite sure there's something wrong in my Javascript, but what can it be?


Issue · Github
by Sheila

Issue Number
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Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @johnma, I haven't used the JS expressions myself yet, so I'm not super familiar with the syntax. I think @lindenb is the one who added this functionality, perhaps he can help you. To aid in the process, could you show a test example of reads that you expect to pass the filter?

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