Output Bedpe question

[jgockley62]

Hi,

In the out put bedpe file does phase indicate genotype as well? ie:
a phase of 1,1 = Homozygous
a phase of 1,!1 = Heterozygous

This could be a stretch but I'm trying to convert the output bedpe to vcf format, any help on that front would most appreciated.

Thanks!

[relyanow]

This is basically right. 1,1 and 2,2 are homozygous. 1,2 and 2,1 are heterozygous. 0 means one strand is not phased. So 1,0 could be either homozygous or heterozygous. Hope that helps!