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This invocation will process `input.bam` with mapping quality threshold=1, write the outputs as two fastq and one longqname files starting with `prefix` by appendig
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`sample_name` into qnames.
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`bam-to-truth` is a program that given bam file and mapping quality threshold with sample_name,
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the reads having mapping quality above the threshold with their paired mate having mapping quality higher than the threshold are together output .
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If no paired mate is found,just outputs the read if mapping quality is above the threshold.The read and it's mate also has to be mapped and be on the same chromosome.
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For qname format, please check the section in the appendix.
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Sometimes we want to treat the alignment from one aligner (e.g. BWA) as the truth and then check how other aligners do, just for comparison sake.
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An ideal tool would do a read by read comparison, and we have some other tools that do this, however, such comparisons
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because they need to matchup read qnames, can become expensive. This is a compromise method.
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