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Use the -X flag in "samtools view" to convert the flag column from a numeric bit field to letters (as described here) like this: % samtools view -Xf 0x10 accepted_hits. This pipeline is intended for calling variants in samples that are.
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  • -s For the overlapping section of a read pair, count only the bases of the first read.
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    Filter alignment records based on BAM flags, mapping quality or.

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