phase having trouble reading the .inp file from VCFtoPHASE

[lisabang]

Hi,

I seem to be having an issue trying to have PHASE read the end results of this conversion tool; is it to do with the fact that the input specifications for PHASE ask for "P" to be given in a single line at some point, and this is read erroneously as a locus type? the output ("conv103_stevison_all.out") is an empty file.

output below:

[gbang@kimlab phase.2.1.1.linux]$ ./PHASE conv103_stevison_all.inp conv103_stevison_all.out
Reading in data
Reading Positions of loci
Invalid locus type P
Must be either 'S' or 'M'

[vidhya-iyer]

While the vcf is getting converted to .inp in the locus type it prints is only S. The perl code itself does not have a way to detect multiallelic sites and print M. So PHASE software is not taking the .inp input.