Advice on how to run phASER with RNA-seq data only and posed genotypes of parents

[apfuentes]

Hi @secastel,
Thanks for developing this neat tool!

We have RNA-seq data of six F1 individuals and would like to perform ASE analysis. Unfortunately we do not have DNA-seq of the F1 individuals, but we do for a variety of 79 individuals from other populations, including the 2 parents used for making the crosses to obtain the F1 offspring. The genotypes of the 79 individuals were phased with BEAGLE (population statistical phasing).

Question:

1. Would it be OK to run phASER separately for each F1 individual and use the same VCF file of 79 individuals with phased genotypes? I understand phASER expects VCF with he genotypes of each sample separately, but perhaps the VCF of 79 individuals offers the best phased genotype data we could get at the moment

2. Or would it be better to perform SNP calling on the RNA-seq data of the six F1 individuals, then phase their genotypes with BEAGLE, then subset the VCF to get one VCF for each sample?

Thanks for your advice

Best,

[secastel]

phASER will only work if you use genotype data that matches the RNA-seq data, so you should not use genotype data from other individuals. For the individuals you are interested in that only have RNA-seq data, I would suggest performing SNP calling using the RNA-seq data and then phasing the genomes using the parental genomes. I'm assuming you are working with a diploid organism, so you would want something like trio phasing to do this.