Introduced the "metahaplome" at #RSGUK15 at @GenomeAnalysis today. You heard it here first! pic.twitter.com/ejiFyUnyRw
— Sam Nicholls (@samstudio8) October 7, 2015
Status Report: February 2016
The adventure continues, here’s what I’m working on lately.
Meet the Metahaplome
Yesterday, I gave a talk at the Aberystwyth Bioinformatics Workshop on the metahaplome: a graph inspired structure for encoding the variation of single nucleotide polymorphisms (SNPs) observed across aligned sequenced reads.
How (not) to subset a BAM for GATK
I wanted a BAM that contained reads aligned to just one of the many contigs the file contained. As usual, I made this much more difficult than it really ought to have been.
Duplicate definition error with GATK PrintReads and MalformedReadFilter
This afternoon I wanted to quickly check whether some reads in a BAM would be filtered out by the GATK `MalformedReadFilter`. Turns out that GATK is pretty unforgiving if you forget that filter is automatically applied by `PrintReads`.
Grokking GATK: Common Pitfalls with the Genome Analysis Tool Kit (and Picard)
Recently I’ve been following the GATK DNASeq Best Practice Pipeline for my limpet sequence data. Here are some of the mistakes I made and how I made them go away.
Metahaplome
The Tolls of Bridge Building: Part IV, Mysterious Malformations
Following a short hiatus on the sample un-improvement job which may or may not have been halted by vr-pipe inadvertently knocking over a storage node at the Sanger Institute, our 837 non-33 jobs burst back in to life only to fall at the final hurdle of the first pipeline of the vr-pipe workflow. Despite my […]
The Tolls of Bridge Building: Part III, Sample (Un)Improvement
Previously, on Samposium: I finally had the 870 lanelets required for the sample improvement process. But in this post, I explain how my deep-seated paranoia in the quality of my data just wasn’t enough to prevent what happened next. I submitted my 870 bridged BAMs to vr-pipe, happy to essentially be rid of having to […]
The Tolls of Bridge Building: Part II, Construction
Last time on Samposium, I gave a more detailed look at the project I’m working on and an overview of what has been done so far. We have 870 lanelets to pre-process and improve into samples. In this post, I explain how the project has turned into a dangerous construction site. While trying to anticipate […]
The Tolls of Bridge Building: Part I, Background
I’m at the Sanger Institute for just another two weeks before the next stop of my Summer Research Tour and it’s about time I checked in. For those of you who still thought I was in Aberystwyth working on my tan1 I suggest you catch up with my previous post. The flagship part of my […]