I have a list of SNPs, and I know number of tags covering these SNPs.
What I intend to find further, is whether the SNPs are homozygous or heterozygous from RNA-Seq tag counts.
I have also computed the RNA-Seq tag counts for each of the SNP, like below:
bedtools multicov -bams RNA1.sort.bam RNA2.bam -bed Cordinate.SNP.txt
RNA-seq I have is a paired end.
Could anyone help, in figuring out if these SNPs are homo or heterozygous based upon the RNA-seq tags covering them.