Retrieve reads overlapping indels
I am doing allelic-specific RNA-seq analysis. Given a list of variants, is there an efficient program to separate reads at each variant position based on whether the variant is present? (especially for variant=indels since they accounted for 10% of my variant list). This looks quite obvious when visualized by IGV but I did not find a program doing it.
(Note: preferably I will need the output to be reads instead of other summarized statistics
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