Comments on: The Tolls of Bridge Building: Part IV, Mysterious Malformations https://samnicholls.net/2015/08/27/bridgebuilding-p4/ The Exciting Adventures of Sam Mon, 18 Jan 2016 12:03:28 +0000 hourly 1 https://wordpress.org/?v=5.7.5 By: How (not) to subset a BAM with GATK and Picard | Samposium https://samnicholls.net/2015/08/27/bridgebuilding-p4/#comment-14 Sun, 10 Jan 2016 22:28:49 +0000 http://blog.ironowl.io/?p=148#comment-14 […] wouldn’t be until later whilst investigating issues with another tool that I would discover how to correctly update the bit flags and read attributes to mark reads as unmapped as per the BAM specification. But in this instance, the error made me question whether I really […]

]]> By: Duplicate definition error with GATK `PrintReads` and `MalformedReadFilter` | Samposium https://samnicholls.net/2015/08/27/bridgebuilding-p4/#comment-13 Thu, 07 Jan 2016 19:27:29 +0000 http://blog.ironowl.io/?p=148#comment-13 […] course, from my own blog post and the PrintReads manual page, I should have recalled that the MalformedReadFilter is […]

]]> By: Grokking GATK: Common Pitfalls with the Genome Analysis Tool Kit (and Picard) | Samposium https://samnicholls.net/2015/08/27/bridgebuilding-p4/#comment-12 Wed, 11 Nov 2015 16:45:18 +0000 http://blog.ironowl.io/?p=148#comment-12 […] touched on this discovery that the GATK MalformedReadFilter is much more aggressive than its documentation lets on previously. The lovely GATK developers have even opened an issue about it after I reported it in […]

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