Hi there, I am using whatsHap to phase my filtered variants. The job was ran well and the output file generates normally. But when I was checking the contents of file, I found only a small proportion of SNPs has been phased. Anybody know why whatsHap didn't phase all SNPs, or is there some mechanism make this limit?
This screenshot was produced through "diff \ -biw \ bcftools_QUAL78_sample_1.vcf \ Phased_Q78_Horti_sample_1.vcf" which represents the phases part ("/" replaced by "|")
While other SNPs were still unphased.
Many thanks, Zitian