Hello, thank you very much for your response. I was referring more to using these options:
-a INT Maximum insert size for a read pair to be considered being mapped properly. Since 0.4.5, this option is only used when there are not enough good alignments to infer the distribution of insert sizes. [500]
-o INT Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing. [100000]
-P Load the entire FM-index into memory to reduce disk operations (base-space reads only). With this option, at least 1.25N bytes of memory are required, where N is the length of the genome.
-n INT Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]
-N INT Maximum number of alignments to output in the XA tag for discordant read pairs (excluding singletons). If a read has more than INT hits, the XA tag will not be written. [10]
-r STR Specify the read group in a format like ‘@RG\tID:foo\tSM:bar’. [null]"
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