Truncate unevenly covered BAM file at certain coverage
This is basic enough question, but I can't seem to find the answer online.
I have a BAM from RNA-seq alignment which is very unevenly covered. However the mean coverage is huge (~100,000x - it's a mitochondrion). I want to use it for polishing, so I would like to retain about 100x "sliding window" (or simply at any given nucleotide) coverage across the whole chromosome, and lose the rest.
How can I achieve this?
Thank you in advance, as always
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