<p>How much does it cost to align a 8 lanes of a HiSeq 2000 flowcell paired-end run consisting of 6 billion 100bp human genomic reads (600Gbp output) using the Amazon EC2 and associated storage?</p>

<p>Assume using an aligner such as BWA with default parameters, aligned against a human reference. Please compute the cost and time from upload of FASTQ files to download of BAM files inclusive.</p>

<p>"It depends" is not a useful answer - if there is a factor such as instance-type or EBS vs S3 please select a sensible option and provide a quote.</p>

<p><a href="https://twitter.com/konrad_jk">Konrad Karczewski</a> of <a href="http://stormseq.org">stormseq</a> said in a recent tweet that "a full genome (30X coverage)  is about $30 or so, exome (80X coverage) is around $2-3." I think this is from fastq-&gt;vcf using BWA and GATK.</p>

<p>Assuming an 80X exome is about 40M reads, a $2.50 exome comes out to about $6.25/hmmvr (hundred million mapped variant reads - my awesome new metric), or about $375 for a HiSeq 2k flowcell. Granted this is going all the way to VCF but that number is in line with what I've heard elsewhere.</p>

<p>I think the BWA-&gt;GATK pipeline is commoditized enough that providers should be using these $/hmmvr on <a href="http://www.scienceexchange.com">scienceexchange</a>. Then labs will have something to compare it with, if they don't want to try AWS themselves.</p>
