Searching for SNPs with cloud computing

[Ben Langmead]

Searching for SNPs with cloud computing
Ben Langmead , Michael C Schatz , Jimmy Lin , Mihai Pop and Steven L Salzberg

Genome Biology 2009, 10:R134
doi:10.1186/gb-2009-10-11-r134

Published: 20 November 2009

Abstract:

As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sf.net/crossbow.

[VIX_Z]

Crossbow on local cluster

HI,
I want to try crossbow on my local cluster and I am looking for the sample dataset. In example mentioned in local/crossbow.pl it is explained with paired human data (reads, reference genome, bowtie index and reference snp file),
Can anybody suggest some link to get such dataset?
Whether all files mentioned in example are compulsory to run crossbow successfully? or can I run it without reference snp file?

Thanks in advance...
Vix

[[email protected]]

soapsnp parameters

I am able to use crossbow 1.1.2 with hadoop.
Would you please let me know what kind of parameters I have to pass to soapsnp/crossbow to

1) significantly reduce amount of false hits
2) not to miss majority of true hits (SNVs)

Many thanks in advance.
best regards,
Mahmoud