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Be aware that some downstream tools (for example the Picard suite, often used before SNP calling) do not like it when a read name appears more than once in the SAM file. Such reads can be filtered, but only if they can be identified as secondary by specifying the bwa mem -M option as we did above. This option leaves the longest alignmen normally but marks additional alignments for the read as secondary (the 0x100 BAM flag). This designation also allows you to easily filter the secondary reads with samtools view -F 0x104 if desired.

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