SNP calling bug

[W. Evan Johnson]

Nate,

Have found a bug in the SNP calling sgrex:

chrX 618045 3.00000 3.00000 0.00000 0.00000 0.00000 0.00000 Y:a->a/a p_val=4.78e-04
chrX 783180 4.00000 0.00000 0.00000 3.99989 0.00011 0.00000 Y:a->g p_val=3.33e-04
chrX 873684 3.00000 3.00000 0.00000 0.00000 0.00000 0.00000 Y:a->a/a p_val=4.78e-04
chrX 1470188 4.00000 0.00000 0.00000 4.00000 0.00000 0.00000 Y:c->g p_val=3.33e-04
chrX 1547378 3.00000 3.00000 0.00000 0.00000 0.00000 0.00000 Y:a->a/a p_val=4.78e-04

Note the Y:a->a/a should not be a SNP!

Thanks!

Evan

[Nathan Clement]

Evan,

Yes. This was a bug. I was looking at the value of the highest nucleotide, then finding the second highest. Since all other locations were zero, it would return the first location (which is also the highest value).

I've fixed it and updated marylou's build (/fslgroup/fslg_genome/software/gnumap_MPI/bin/gnuamp). Let me know if you want me to create a different version for this.

Nathan

[W. Evan Johnson]

Thanks Nate. Not a problem. I just filtered them out myself, but didn't want for this to confuse others. Thanks for all your efforts!