How to get MD tag sequence of a read from a sam file given a bed file?
Hello! I am attempting to get a MD tag sequence from a read given a bed file with start and stop positions. For example, my sam file has a read like:
chr1 0 chr1 78142606 60 78278871S73M2D...
and I have a bed file with a line like:
chr1 78142736 78143236
I want to get the sequence from indexed position 78142736-78143236 so that I can calculate a percent identity score for that specific bin. I've attempted using samtools view but I can't seem to get it to do what I want it to. Please help!
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aw7 •
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n.a.tekkey •
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What was the exact options you used with samtools view and what were the results?