gravatar for Istvan Albert

1 hour ago by

University Park, USA

Have the flags explained

samtools flags 2304

then -f means:

 -f INT   only include reads with all  of the FLAGs in INT present [0]

can an alignment be both secondary and supplementary at the same time? These are mutually exclusive terms.

If you wanted to include only the non-primary alignments and that you would need to do it in two steps.

First select the secondary, then the supplementary.

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