Bored to death seeing public releases of sequencing runs from E. Coli coming off desktop sequencers? Today, Life Technologies released through the Ion Community a sequencing run that wasn’t from E. Thank goodness. Ion Torrent released a human shotgun sequencing run from (aka Venter published in ). Unfortunately, it was only two separate runs (C18-99 and C24-141) from a 318 chip so has bugger all in terms of coverage.

I am extremely grateful for the release of the data set (kudos to Matt in Life Tech for the early access:D), though it would have been much nicer if they released results from a custom capture because at least it wouldn’t be totally useless for analysis. However, all is not lost as the coverage from the mitochondrial genome was sufficient to do some analysis (Figure 1). Shows the coverage (determined by BEDtools) from using the two supplied BAMs.

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The coverage output for bwa-sw aligned BAMs produces an almost identical coverage and produces a bit of a mess when it is plotted also. Installing A Headlight Visor more. Mitochondrial variants What’s made the analysis of the mitochondrial genome (chrM) a bit annoying is that the two BAM files supplied don’t appear to be aligned to a hg19 chrM reference. According to the BAM header the chrM it was aligned to was 16569 bases in length (@SQ SN:chrM LN:16569).

This is two bases less than the or obtained from UCSC Genome Browsers. Since I was missing this version of chrM I decided to create my own alignments using bwa-sw, in addition to using tmap and subsequent base calling performed by the The table below shows the results (tmap alignment of C24 is missing as it was still grinding away, while writing this 😕 Variants Called C18-99 (VCF supplied) 29 (including 3 INDELS) C24-141 (VCF supplied) 30 (including 3 INDELS) C18-99 (bwa-sw/GATK) 41 C24-141 (bwa-sw/GATK) 39 C18-99 (tmap/GATK) 35 It is hard to determine the overlap between the variants called by the supplied VCF (i.e. Pantone Color Manager Serial Number more. By mpileup) and the ones called by GATK as the differences between the two reference chrM creates an off by 1-2 base difference in the coordinates. On inspection the majority of the mpileup calls are due to differences between the two references evident in what is marked as the ref or alt base. Below is the Venn diagram showing the variants called by GATK between the two runs. Using the, the variants outside the intersection had reads supporting it on the run which it was not called on.