Zero counts for haplotypes

[aswathyseb]

Hi Stephane,

Could you please help me understand why do I get 0 counts for one of the haplotype?

Attached here is the IGV screenshot of the region chr1:34616-40204 (Zm00001eb000010) which shows the counts should be 11 and 14. But phASER gave me 15 and 0. phASER output is also attached here.

I would really appreciate your comments.
Thank you
Aswathy
sample_gene_ae.txt