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ASEReadCounter contruct a heterozygous VCF input file for all nucleotides in region of interest
The aim is to identify any and all bi-allelic SNPs in my region of interest.
Then determine if there is allelic imbalance in all my RNA-seq samples.
I already filtered the BAM files for the region of interest and managed to produce a vcf file for the matching region.
However the documentation for the ASEReadCounter states that the input:
"A VCF file with specific sites to process."
Is it possible to construct a vcf file (of my region of interest) where I have bi-allelic information for every single base? How can this be done since there would be 3 different alternative alleles? Would this actually work in ASEReadCounter?
I'm trying to avoid making a vcf file for each sample and using the same vcf file as input for ASEReadCounter. Do I have the right understanding? In other words, where does the original vcf input file come from?