SNP Allele Designations (Bio::SNP::Inherit)

Christopher BottomsBOSC 2010

5 million data “items”

one CPU: 2+ dayseight CPUs: 1-2 days

SNP ID Sample ID Base1 Base21 1 A A1 2 A A1 3 A G… … … …1 5000 A A2 1 C C… … … …… … … …1106 5000 GG GG

SNP ID Sample ID Base1 Base21 1 A A1 2 A A1 3 A G… … … …1 5000 A A2 1 C C… … … …… … … …1106 5000 GG GG

“Matrix” data file format

SNP ID 1 2 3 … 5000SNP1 AA AA AG … AASNP2 CC GG GG … CG

“Matrix” data file format

SNP ID 1 2 3 … 5000SNP1 AA AA AG … AASNP2 CC GG GG … CG

Using new data format

12 million data itemsone cpu: ~30 min

ID’s fileID Name Group

1 B73 B73

2 B73xZ1 NAMF1

3 Mo17 Control

4 M100 IBM

5 Bob B73xZ1

ID’s fileID Name Group

1 B73 B73

2 B73xZ1 NAMF1

3 Mo17 Control

4 M100 IBM

5 Bob B73xZ1

“Human Parsed” ID’s fileID Name Group A (ID) B (ID) AxB (ID)

1 B73 B73

2 B73xZ1 NAMF1

3 Mo17 Control

4 M100 IBM 1 3

5 Bob B73xZ1 1 2

Lessons learned

Explore other solutions before deciding on parallel processing

File format changes can simplify work

When appropriate, divide workHumans: Complicated but “once-only” taskComputers: Repetitive boring work

AcknowledgementsAdvisors

Mike McMullenSherry Flint-Garcia

Hardware supportArturo Garcia

FundingNational Science Foundation Plant Genome Program

Grant DBI-0820619USDA-ARS

AcknowledgementsProgramming support

You (CPAN)You (stackoverflow.com)You (perlmonks.org)

End