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Old 05-17-2019, 04:03 AM   #222
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,976
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I think you are looking for the following options that are accessible from "reformat.sh".

Code:
Sam and bam processing options:

mappedonly=f            Toss unmapped reads.
unmappedonly=f          Toss mapped reads.
pairedonly=f            Toss reads that are not mapped as proper pairs.
unpairedonly=f          Toss reads that are mapped as proper pairs.
primaryonly=f           Toss secondary alignments.  Set this to true for sam to fastq conversion.
minmapq=-1              If non-negative, toss reads with mapq under this.
maxmapq=-1              If non-negative, toss reads with mapq over this.
requiredbits=0          (rbits) Toss sam lines with any of these flag bits unset.  Similar to samtools -f.
filterbits=0            (fbits) Toss sam lines with any of these flag bits set.  Similar to samtools -F.
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