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letamp;#39;s start so we will say BCF tools letamp;#39;s just display the files again here we need a sorted bump file so we will say BCF tools you see M pile up Dash o Thatamp;#39;s SB we need the output to be in the BCF formats and then we also indicates Dash o for the output file so letamp;#39;s say raw.pcf and then we also need to indicate the ref okay thatamp;#39;s the reference genome so thatamp;#39;s just uh f and then we indicates ref Dash ref slash Agy we need a four parts so that is what we are going to use here so we need that information so we need the dash F4 thatamp;#39;s and then we also need threads so you see threads you can decide to relive it but you can also add it and then just speed up your work so letamp;#39;s use it and then here you can also do some filtering so that skill can be used to exclude bases okay thatamp;#39;s half quality slower than a particular pressure so letamp;#39;s say we want to remove or exclude bases with qualities and lower or belo
