Q:

I am looking for a tool to detect allele specific expression from resequencing and RNA-seq data. I find AlleleSeq could be quite powerful. I noticed the input for the software needs parents genotype data; it requires a VCF file which contains trio genotype to create maternal and paternal genome. But in my case, if I only have genotype information from a single individual, how could I use AlleleSeq?

A:

You dont have to genotype parents. You only need to have variants phased in any way you can/wish (vcf2diploid tool only looks at one column with info for the individual of interest and does not consider other columns). Having trio sequenced is an easy and, probably, the best way to do it.

If you have the mothers genotype only, then you can phase a good fraction of heterozygous variants. Each unphased variants will be randomly assigned to a particular haplotype, so half of them will also be correct. And, of course, all homozygous variants will be phased.