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- -q N – only report alignment records with mapping quality of at least N (>= N).
- -f 0xXX – only report alignment records where the specified flags are all set (are all 1)
- you can provide the flags in decimal, or as here as hexadecimal
- -F 0xXX – only report alignment records where the specified flags are all cleared (are all 0)
Setup
Login to ls6.tacc.utexas.edu and start an idev session.
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