I wanted to ask if I can use ASE read counter on WXS data, instead of RNA seq. Would it give me the number of times a particular SNP has been observed on the DNA level? And is it correct to interpret the results that way?
Oh, no I don't think that would be appropriate -- it'll be vulnerable to biases inherent in the exome capture technology, I wouldn't trust the results. But GATK4 has some new methods for allelic copy number variation that you should probably check out -- see the GATK4 Beta section of the forum.
Are you looking for allelic depth observed in sequencing?
No I'm hoping to use it as a proxy for copy number alterations per allele (does allele A seem to have more copies than Allele B ), need it for a quick analysis.