Pharmacogenetics of Asthma Treatment

The Phase2best tool takes a set of haplotype strings as input. It has very flexible input processing, which can cope with several formats:

I. Phase Output

For example, you can cut and paste the haplotypes from a phase output file (from running phase on your own data or using our phase tool) and run the best algorithm, producing a report showing all of the minimum cardinality sets of htSNP together with the binary equivalents

To test it, you can cut and paste the following haplotypes taken from the phase output for CARD4/NOD1 into the text box and click the "Do it!" button to find the 5 htsnp:

1: G A C G T G T G G G T A C G G T T T G C G A T A C A C C G A C (2)
2: G G T A T G T A C A C G C G A T T T G T A G T A C A C C G A C (2)
3: G G T A T G T A C A C G C G G T T T G C G A T A C A C C G A C (21)
4: G A C G T G T G G G T A C G A T T T G C G A T A C A C C G A C (4)
5: G G T A C G T A C A C G C G G C T C A C G A T A C A C C G A C (8)
6: G G T A T G T A C A C G C G G T T C G T A A T G T G C C G G T (2)
7: G G T A T G T A C A C G C G G T T T G C A A T A C A C C G A C (1)
8: G A C G T G T G G G T A C G A T T C G C G A T A C A C C G A C (2)
9: G A C G T G T G G G T A C G A T T C A C G A T A C A C C G A C (1)
10: G A C G T G T A G G T A C G A T T T G C G A T A C A C C G A C (1)

II. "Johnson" format

It also takes haplotypes in the format Johnson used in her htSNP paper with common alleles as ".":

GACGGGCCAGAT+TG+TGCTCC (31)
...............-.AT... (18)
......T..C....A-..T..G (15)
AG..A..TG.TC.C.-C.T..G (14)
.G.C.A.T.......-..T... (10)
..T............-..T... (6)
...............-..T... (2)
............-..-...CTG (2)
AG..A..TG.TC...-C.T..G (1)
AG..A..TG.TC.C.-CAT... (1)

III. Plain strings

Finally, if you cut off the last 2 numeric columns from SNPHAP output, it will also process those. For example, these are the >2% haplotypes from BPI, which you could cut/paste into phase2best:

AGCGCAGGAAGGTGAGGGA   
GCTCCGAGAGAGCGGAAAG   
GCTCGGAGAGAGCGGAAAG   
GCTCCAGGGGACCAAGGGA   
GCTGCGAGAGAGCGGAAGA   
GCTCCAGGAAGGCGAGGGA   
AGCGCAGGAAGGTGGAAAG   
GCTCCGAGAGAGCGGAAGA   
GCTCCGAGAGAGCGAGGGA   
GCTCCGAGAGAGTGAGGGA   
GCTCCAGGAAGGTGAGGGA   

IV. Prettybase format

We recently added a Prettybase to SNPHAP tool, which can process the haplotypes estimated by Clayton's SNPHAP and return the BEST report directly. To use that tool, your genotype data must be in Nickerson's "prettybase" format.